Duplexed parvovirus vectors

ABSTRACT

The present invention provides duplexed parvovirus vector genomes that are capable under appropriate conditions of forming a double-stranded molecule by intrastrand base-pairing. Also provided are duplexed parvovirus particles comprising the vector genome. Further disclosed are templates and methods for producing the duplexed vector genomes and duplexed parvovirus particles of the invention. Methods of administering these reagents to a cell or subject are also described. Preferably, the parvovirus capsid is an AAV capsid. It is further preferred that the vector genome comprises AAV terminal repeat sequences.

RELATED APPLICATION INFORMATION

The present invention is a continuation of U.S. application Ser. No.11/655,520 (now U.S. Pat. No. 7,790,154 B2) having a filing date of Jan.19, 2007, which is a divisional of U.S. application Ser. No. 10/276,356(now U.S. Pat. No, 7,465,583 B2), which is a 35 U.S.C. §371 nationalphase application of PCT Application No, PCTUS01/17587, having aninternational filing date of May 31, 2001, and which claims priority toU.S. Provisional Patent Application No. 60/208,604, filed Jun. 1, 2000,the entire contents of each of which are incorporated by referenceherein.

STATEMENT OF FEDERAL SUPPORT

The present invention was made, in part, with the support of grantnumbers HL51818, HL 48347, and DK 54419 from the National Institutes ofHealth. The United States government has certain rights to thisinvention.

FIELD OF THE INVENTION

The present invention relates to reagents for gene delivery. Moreparticularly, the present invention relates to improved parvovirus-basedgene delivery vectors.

BACKGROUND OF THE INVENTION

Adeno-associated virus (AAV) is a nonpathogenic, helper dependent memberof the parvovirus, family. One of the identifying characteristics ofthis group is the encapsidation of a single-stranded DNA (ssDNA) genome.In the case of AAV, the separate plus or minus polarity strands arepackaged with equal frequency, and either is infectious. At each end ofthe ssDNA genome, a palindromic terminal repeat (TR) structurebase-pairs upon itself into a hairpin configuration. This serves as aprimer for cellular DNA polymerase to synthesize the complementarystrand after uncoating in the host cell. Adeno-associated virusgenerally requires a helper virus for a productive infection. Althoughadenovirus (Ad) usually serves this purpose, treatment of AAV infectedcells with UV irradiation or hydroxyurea (HU) will also allow limitedreplication.

Recombinant AAV (rAAV) gene delivery vectors also package ssDNA of plusor minus polarity, and must rely on cellular replication factors forsynthesis of the complementary strand. While it was initially expectedthat this step would be carried out spontaneously, by cellular DNAreplication or repair pathways, this does not appear to be the case.Early work with rAAV vectors revealed that the ability to score markergene expression was dramatically enhanced when cells were co-infectedwith adenovirus, or transiently pretreated with genotoxic agents. Thisenhancement correlated with the formation of duplex DNA from thesingle-stranded virion DNA (vDNA). Similar induction of rAAV vectors hasbeen observed in vivo following treatment with Ad, ionizing radiation,or topoisomerase inhibitors. However, the effect was highly variablebetween different tissues and cell types. It has more recently beensuggested that reannealing of complementary vDNA from separate infectingrAAV particles may be an important pathway for rAAV transduction.

The requirement for complementary-strand synthesis, or recruitment, isnow considered to be a limiting factor in the efficiency of rAAVvectors. The transduction rate for rAAV in mouse liver has beenestimated at approximately 5% of hepatocytes after portal vein infusionof 4.2×10¹⁰ particles. Subsequent experiments revealed that the rAAVvDNA had been taken up into the nuclei of virtually all of the liverhepatocytes, and that the transduction potential of these genomes couldbe rescued by co-infection with adenovirus. This is consistent with anearlier report of up to 25% of mouse hepatocytes transduced by 10¹⁰particles of rAAV in the presence of co-infecting adenovirus. Expressionfrom rAAV in liver tissue coincides with the formation of duplex DNA andthe vDNA appears to be lost if not converted to duplex within 5-13weeks. Further experiments suggest that a subpopulation of mousehepatocytes is transiently permissive for rAAV transduction in vivo.

Accordingly, the present invention addresses a need in the art forimproved parvovirus gene delivery vectors. In particular the presentinvention addresses the requirement for complementary strand synthesisby conventional AAV gene delivery vectors.

SUMMARY OF THE INVENTION

The single-stranded nature of the AAV genome may impact the expressionof rAAV vectors more than any other biological feature. Rather than relyon potentially variable cellular mechanisms to provide acomplementary-strand for rAAV vectors, it has now been found that thisproblem may be circumvented by packaging both strands as a single DNAmolecule. In the studies described herein, an increased efficiency oftransduction from duplexed vectors over conventional rAAV was observedin HeLa cells (5-140 fold). More importantly, unlike conventionalsingle-stranded AAV vectors, inhibitors of DNA replication did notaffect transduction from the duplexed vectors of the invention. Inaddition, the inventive duplexed parvovirus vectors displayed a morerapid onset and a higher level of transgene expression than did rAAVvectors in mouse hepatocytes in vivo. All of these biological attributessupport the generation and characterization of a new class of parvovirusvectors (delivering duplex DNA) that significantly contribute to theongoing development of parvovirus-based gene delivery systems.

Overall, a novel type of parvovirus vector that carries a duplexedgenome, which results in co-packaging strands of plus and minus polaritytethered together in a single molecule, has been constructed andcharacterized by the investigations described herein. Accordingly, thepresent invention provides a parvovirus particle comprising a parvoviruscapsid (e.g., an AAV capsid) and a vector genome encoding a heterologousnucleotide sequence, where the vector genome is self-complementary,i.e., the vector genome is a dimeric inverted repeat. The vector genomeis preferably approximately the size of the wild-type parvovirus genome(e.g., the MV genome) corresponding to the parvovirus capsid into whichit will be packaged and comprises an appropriate packaging signal. Thepresent invention further provides the vector genome described above andtemplates that encode the same.

As a further aspect, the present invention provides a duplexedparvovirus particle comprising: a parvovirus capsid and a vector genomecomprising in the 5′ to 3′ direction: (i) a 5′ parvovirus terminalrepeat sequence; (ii) a first heterologous nucleotide sequence; (iii) anon-resolvable parvovirus terminal repeat sequence; (iv) a separateheterologous nucleotide sequence that is essentially completelycomplementary to the first heterologous nucleotide sequence; and (v) a3′ parvovirus terminal repeat sequence; wherein the vector genome iscapable under appropriate conditions of intrastrand base-pairing betweenthe heterologous nucleotide sequences upon release from the parvoviruscapsid. A double-stranded sequence is formed by the base-pairing betweenthe complementary heterologous nucleotide sequences, which is a suitablesubstrate for gene expression (i.e., transcription and, optionally,translation) or a substrate for host recombination (i.e., a dsDNAtemplate) in a host cell without the need for host cell machinery toconvert the vector genome into a double-stranded form.

The designations of 5′ and 3′ with respect to the vector genome (ortemplates for producing the same, see below) does not indicate anyparticular direction of transcription from the double-stranded sequenceformed between the two complementary heterologous sequences. The “codingstrand” may be on either the 5′ or 3′ half of the virion DNA. Thoseskilled in the art will appreciate that the term “coding strand” isbeing used in its broadest sense to indicate the strand encoding thedesired transcript, and encompasses non-translated sequences as well,including antisense sequences. Thus, transcription may be initiated fromthe 5′ end of the first heterologous nucleotide sequence in the 5′ halfof the vector genome, or from the 5′ end of the complementaryheterologous nucleotide sequence on the 3′ half of the vector genome.

Alternatively stated, in the double-stranded vDNA formed by intrastrandbase-pairing, transcription may be initiated from the open end or fromthe closed end (i.e., from the end closest to the non-resolvable TR) ofthe hairpin structure.

According to this embodiment, the parvovirus capsid is preferably an AAVcapsid. It is further preferred that the parvovirus terminal repeatsequences and/or the non-resolvable terminal repeat sequences are AAVsequences.

In particular embodiments, the duplexed parvovirus particle comprisessufficient expression control sequences (e.g., a promoter) forexpression of the double-stranded sequence formed by intrastrandbase-pairing in the self-complementary vDNA.

The vector genome may further express two or more transcripts from thedouble-stranded sequence formed by intrastrand base-pairing.

As a further aspect, the present invention provides a nucleotidesequence comprising a template for producing a virion DNA, the templatecomprising a heterologous nucleotide sequence flanked by a parvovirusterminal repeat sequence and a non-resolvable parvovirus terminal repeatsequence.

As a still further aspect, the present invention provides a nucleotidesequence comprising a dimeric template for producing a virion DNA, thetemplate comprising in the 5′ to 3′ direction: a 5′ parvovirus terminalrepeat sequence; a first heterologous nucleotide sequence; anon-resolvable parvovirus terminal repeat sequence; a separateheterologous nucleotide sequence that is essentially completelycomplementary to the first heterologous nucleotide sequence; and a 3′parvovirus terminal repeat sequence; wherein the virion DNA is capableunder appropriate conditions of intrastrand base-pairing to form a dsDNAbetween the heterologous nucleotide sequences upon release from theparvovirus capsid.

Preferably, the parvovirus terminal repeat sequences and/or parvovirusnon-resolvable terminal repeat sequences are AAV sequences.

The present invention further provides methods of producing andadministering the inventive duplexed parvovirus vectors of theinvention. In one particular embodiment, the present invention providesa method of administering a nucleotide sequence to a subject, comprisingadministering to a subject a duplexed parvovirus particle according tothe invention in a pharmaceutically acceptable carrier. Preferably, theduplexed parvovirus particle is administered in atherapeutically-effective amount to a subject in need thereof.

As a further aspect, the present invention provides a method ofdelivering a nucleotide sequence to a cell, comprising: contacting acell with a duplexed parvovirus particle comprising: a parvovirus capsidand a vector genome comprising: (i) a 5′ parvovirus terminal repeatsequence; (ii) a first heterologous nucleotide sequence; (iii) acentrally-located parvovirus terminal repeat sequence; (iv) a separateheterologous nucleotide sequence that is essentially completelycomplementary to the first heterologous nucleotide sequence (v) a 3′parvovirus terminal repeat sequence; wherein the duplexed vector genomeis capable under appropriate conditions of intrastrand base-pairingbetween the heterologous nucleotide sequences upon release from theparvovirus capsid.

According to this embodiment, preferably the parvovirus capsid is an AAVcapsid, and the vector genome is approximately the size of the wild-typeAAV genome. It is further preferred that the parvovirus terminal repeatsequences are AAV sequences. The cell may be contacted with the duplexedparvovirus particle in vitro or in vivo:

These and other aspects of the present invention are described in moredetail in the description of the invention set forth below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Virion DNA content of rAAV and duplexed vectors. The drawingillustrates the DNA content of the vectors used in this study and thepredicted conformation that they adopt upon release from the virions.The transgenes expressed from the cytomegalovirus immediate earlypromoter (CMV) are: green fluorescent protein (GFP), β galactosidase(LacZ), mouse erythropoietin (mEpo). Neomycin phosphotransferase (neo)is expressed from the SV40 early promoter (SV40). The size, innucleotides (nt) of each packaged DNA molecule is indicated. Theself-complementary or duplexed (scAAV) GFP dimer and mEpo vectors foldinto a complete duplex DNA with one extra copy of the terminal repeatwhile the GFPneo, LacZ, and mEpoλ vectors require cell-mediated DNAsynthesis of the complementary strand.

FIG. 2. Vector fractionation on CsCl gradients. Virion DNA (vDNA) wasextracted from CsCl gradient fractionated CMV-GFP (Panel a), GFPneo(Panel b), and LacZ (Panel c) rAAV vectors. Alkaline agarose gels of thevDNA were Southern blotted and hybridized with a CMV-GFP DNA fragment.Markers at the left end of panel a were the excised vector sequencesfrom the plasmids used to generate the viral vectors (see results). Thenumber of unit length, ssDNA, vector copies per molecule are indicatedby 1x, 2x, and 4x. The viral vectors used in the experiments depicted inFIGS. 3 and 4 were from fractions a-11 or a-10 for CMV-GFP (as indicatedin the figure legends), fraction b-13 for GFPneo, and fraction c-12 forLacZ.

FIG. 3. Transduction efficiency of duplexed versus conventional rAAVvectors in the absence and presence of co-infecting adenovirus. Theefficiencies of the three CsCl fractionated vectors (FIG. 1) werecompared in rapidly dividing HeLa cells infected with scAAV-GFP fraction11 (0.5 particles per cell), rAAV-GFPneo fraction 13 (2 particles percell), or rAAV-LacZ fraction 12 (0.5 particles per cell). Transductionwas quantified at 24 hours post-infection by counting GFP positive cellsusing fluorescence microscopy, or by fixing the cells and X-GaI.staining. The transducing efficiency was graphed as the number ofphysical particles per transducing unit, as determined by the number ofcells scoring positive for GFP or LacZ expression. Dark grey barsindicate transducing efficiency in the presence of Ad co-infection at 5pfu per cell.

FIG. 4. Transduction with duplexed and conventional rAAV vectors in thepresence of DNA synthesis inhibitor. (Panel a). HeLa cell cultures at30% confluence were treated with the indicated concentrations ofhydroxyurea 24 hr before infecting with 3.8×10⁶ particles of thescAAV-GFP, ♦, (FIG. 2 a, fraction 10), the homologous monomer, • (FIG.2, panel a, fraction 14), or rAAV-GFPneo, ▴, (FIG. 2, panel b, fraction13). The HU treatment was maintained until transduction was assayed at24 hr post-infection. Each data point was calculated from the mean ofthe number of GFP positive cells in 10 random fields independently ofthe total cell number, which was variable due to the effect ofhydroxyurea on cell division. (Panel b). The same procedure was used toevaluate transduction in the presence of the indicated concentrations ofaphidicolin. Only the duplexed and homologous monomer (fractions 10 and14) were compared.

FIG. 5. In vivo transduction of mouse liver tissue with duplexed orsingle-stranded rAAV vectors. Ten week old Balb-c ByJ mice were infusedwith 2×10¹⁰ particles of either scAAV-CMV-mEpo, ♦, (n=4), or full-lengthsingle-stranded rAAV-CMV-mEpoλ, ▴, (n=5), in 200 μl normal saline byportal vein injection. One group of control mice was infused with normalsaline, □, (n=4), and a single mouse, ◯, was phlebotomized at the same7-day intervals without prior surgery. Blood hematocrit was used as afunctional measure of mEpo expression.

FIG. 6 is a representation of a preferred template for producing theduplexed parvovirus vectors of the invention. The nucleotide sequence ofthe AAV2 terminal repeat is shown (SEQ ID NO: 1). Also shown is an XbaIsite and an insertion of a HpaI site, which can be used to delete theindicated fragment and create a modified terminal repeat with reducedresolution by Rep.

FIG. 7 shows a CsCl density gradient of the rAAV-CMV-GFP Hpa-trs mutantvector.

DETAILED DESCRIPTION OF THE INVENTION

The present invention will now be described with reference to theaccompanying drawings, in which preferred embodiments of the inventionare shown. This invention may, however, be embodied in different formsand should not be construed as limited to the embodiments set forthherein. Rather, these embodiments are provided so that this disclosurewill be thorough and complete, and will fully convey the scope of theinvention to those skilled in the art.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. The terminology used in thedescription of the invention herein is for the purpose of describingparticular embodiments only and is not intended to be limiting of theinvention. As used in the description of the invention and the appendedclaims, the singular forms “a”, “an” and “the” are intended to includethe plural forms as well, unless the context clearly indicatesotherwise. All publications, patent applications, patents, and otherreferences mentioned herein are incorporated by reference in theirentirety.

Nucleotide sequences are presented herein by single strand only, in the5′ to 3′ direction, from left to right, unless specifically indicatedotherwise. Nucleotides and amino acids are represented herein in themanner recommended by the IUPAC-IUB Biochemical Nomenclature Commission,or (for amino acids) by either the one-letter code, or the three lettercode, both in accordance with 37 CFR §1.822 and established usage. See,e.g., Patent In User Manual, 99-102 (November 1990) (U.S. Patent andTrademark Office).

Except as otherwise indicated, standard methods known to those skilledin the art may be used for the construction of recombinant parvovirusand rAAV constructs, packaging vectors expressing the parvovirus repand/or cap sequences, as well as transiently and stably transfectedpackaging cells. Such techniques are known to those skilled in the art.See, e.g., SAMBROOK et al., MOLECULAR CLONING: A LABORATORY MANUAL 2ndEd. (Cold Spring Harbor, N.Y., 1989); F. M. AUSUBEL et al. CURRENTPROTOCOLS IN MOLECULAR BIOLOGY (Green Publishing Associates, Inc. andJohn Wiley & Sons, Inc., New York).

Parvoviruses are relatively small DNA animal viruses and contain alinear, single-stranded DNA genome. The term “parvovirus” as used hereinencompasses the family Parvoviridae, including autonomously-replicatingparvoviruses and dependoviruses. The autonomous parvoviruses includemembers of the genera Parvovirus, Erythrovirus, Densovirus, Iteravirus,and Contravirus. Exemplary autonomous parvoviruses include, but are notlimited to, mouse minute virus, bovine parvovirus, canine parvovirus,chicken parvovirus, feline panleukopenia virus, feline parvovirus, gooseparvovirus, and B19 virus. Other autonomous parvoviruses are known tothose skilled in the art. See, e.g., BERNARD N. FIELDS et al., VIROLOGY,volume 2, chapter 69 (3d ed., Lippincott-Raven Publishers).

The genus Dependovirus contains the adeno-associated viruses (AAV),including but not limited to, AAV type 1, AAV type 2, AAV type 3, MVtype 4, AAV type 5, MV type 6, avian MV, bovine MV, canine AAV, equineAAV, and ovine MV. See, e.g., BERNARD N. FIELDS et al., VIROLOGY, volume2, chapter 69 (3d ed., Lippincott-Raven Publishers).

As used herein, the term “vector” or “gene delivery vector” may refer toa parvovirus (e.g., AAV) particle that functions as a gene deliveryvehicle, and which comprises vDNA (i.e., the vector genome) packagedwithin a parvovirus (e.g., AAV) capsid. Alternatively, in some contexts,the term “vector” may be used to refer to the vector genome/vDNA.

A “heterologous nucleotide sequence” will typically be a sequence thatis not naturally-occurring in the virus. Alternatively, a heterologousnucleotide sequence may refer to a viral sequence that is placed into anon-naturally occurring environment (e.g., by association with apromoter with which it is not naturally associated in the virus).

As used herein, a “recombinant parvovirus vector genome” is a parvovirusgenome (i.e., vDNA) into which a heterologous (e.g., foreign) nucleotidesequence (e.g., transgene) has been inserted. A “recombinant parvovirusparticle” comprises a recombinant parvovirus vector genome packagedwithin a parvovirus capsid.

Likewise, a “rAAV vector genome” is an AAV genome vDNA) that comprises aheterologous nucleotide sequence. rAAV vectors require only the 145 baseterminal repeats in cis to generate virus. All other viral sequences aredispensable and may be supplied in trans (Muzyczka, (1992) Curr. TopicsMicrobiol. Immunol. 158:97). Typically, the rAAV vector genome will onlyretain the minimal terminal repeat (TR) sequences so as to maximize thesize of the transgene that can be efficiently packaged by the vector. A“rAAV particle” comprises a rAAV vector genome packaged within an AAVcapsid.

The inventive parvovirus particles may be a “hybrid” particle in whichthe viral TRs and viral capsid are from different parvoviruses.Preferably, the viral TRs and capsid are from different serotypes of AAV(e.g., as described in international patent publication WO 00/28004,U.S. Provisional Application No. 60/248,920; and Chao et al., (2000)Molecular Therapy 2:619; the disclosures of which are incorporatedherein in their entireties). Likewise, the parvovirus may have a“chimeric” capsid (e.g., containing sequences from differentparvoviruses, preferably different AAV serotypes) or a “targeted” capsid(e.g., a directed tropism) as described in international patentpublication WO 00/28004.

Preferably, the inventive duplexed parvovirus particle has an AAVcapsid, which may further by a chimeric or targeted capsid, as describedabove.

The inventive “duplexed” parvovirus particles and vector genomes mayinterchangeably be referred to herein as “dimeric” or“self-complementary” vectors. The duplexed parvovirus particles of theinvention comprise a parvovirus capsid containing a virion DNA (vDNA).The vDNA is self-complementary so that it may form a hairpin structureupon release from the viral capsid. The duplexed vDNA appears to provideto the host cell a double-stranded DNA that may be expressed (i.e.,transcribed and, optionally, translated) by the host cell without theneed for second-strand synthesis, as required with conventionalparvovirus vectors.

The duplexed parvovirus vector genome preferably contains sufficientpackaging sequences for encapsidation within the selected parvoviruscapsid (e.g, AAV capsid).

Those skilled in the art will appreciate that the duplexed vDNA may notexist in a double-stranded form under all conditions, but has theability to do so under conditions that favor annealing of complementarynucleotide bases, Accordingly, the term “duplexed parvovirus vector”does not indicate that the vDNA is necessarily in duplexed ordouble-stranded form (e.g., there is base-pairing between theself-complementary strands) within the parvovirus capsid. Indeed, oneskilled in the art will understand that the vDNA is likely not in adouble-stranded form while packaged within the parvovirus capsid.

Expression of a heterologous nucleotide sequence (as described below) ispreferably “enhanced” from the duplexed parvovirus vectors of theinvention as compared with the comparable parvovirus (e.g., rAAV)vector. Preferably, gene expression may be detected from the duplexedparvovirus vector substantially more rapidly than from the comparablemonomeric parvovirus vector. For example, gene expression may bedetected in less than about 2 weeks, preferably less than about oneweek, more preferably less than about 72 hours, still more preferablyless than about 48 hours, and still more preferably less than about 24hours after administration of the duplexed parvovirus vector. Geneexpression may be detected by any method known in the art, e.g., bydetecting transcription, translation, or biological activity or aphenotypic effect resulting from expression of a heterologous nucleotidesequence (e.g., blood clotting time).

Alternatively, gene expression from the duplexed parvovirus vector maybe “enhanced” in that higher levels of gene expression (as defined inthe preceding paragraph) are detected as compared with the comparablemonomeric parvovirus vector (e.g., rAAV vector). Comparisons may be madein the level of gene expression at the same time point afteradministration of virus. Alternatively, comparisons may be made betweenthe maximum level of gene expression achieved with each vector.

The duplexed parvovirus vectors of the invention may advantageously haveimproved transduction unit (tu) to particle ratios as compared withconventional parvovirus vectors. Accordingly, the present invention alsoencompasses novel parvovirus vector compositions having an improvedtu/particle ratio over compositions of conventional parvovirus vectors(e.g., rAAV vectors). Preferably, the tu/particle ratio is less thanabout 50:1, less than about 20:1, less than about 15:1, less than about10:1, less than about 8:1, less than about 7:1, less than about 6:1,less than about 5:1, less than about 4:1, or lower. There is noparticular lower limit to the tu/particle ratio. Typically, thetu/particle ratio will be greater than about 1:1, 2:1, 3:1 or 4:1.

The term “template” or “substrate” is typically used herein to refer toa polynucleotide sequence that may be replicated to produce the duplexedparvovirus vDNA of the invention. For the purpose of vector production,the template will typically be embedded within a larger nucleotidesequence or construct, including but not limited to a plasmid, naked DNAvector, bacterial artificial chromosome (BAC), yeast artificialchromosome (YAC) or a viral vector (e.g., adenovirus, herpesvirus,Epstein-Barr Virus, AAV, baculoviral, retroviral vectors, and the like).Alternatively, the template may be stably incorporated into thechromosome of a packaging cell.

As used herein, the term “polypeptide” encompasses both peptides andproteins, unless indicated otherwise.

As used herein, “transduction” or “infection” of a cell by AAV meansthat the AAV enters the cell to establish a latent or active (i.e.,lytic) infection, respectively. See, e.g., BERNARD N. FIELDS et al.,VIROLOGY, volume 2, chapter 69 (3d ed., Lippincott-Raven Publishers). Inembodiments of the invention in which a rAAV vector is introduced into acell for the purpose of delivering a nucleotide sequence to the cell, itis preferred that the AAV integrates into the genome and establishes alatent infection.

Duplexed Parvovirus Vectors.

The present invention is based, in part, on the discovery that“duplexed” DNA parvovirus vectors (as described above) can beadvantageously employed for gene delivery. Furthermore, the presentinvestigations have demonstrated that these duplexed parvovirus vectorsmay be more efficient than AAV vectors, e.g., improved transducing toparticle ratios, more rapid transgene expression, a higher level oftransgene expression, and/or more persistent transgene expression. Theinventors have further demonstrated that the duplexed parvovirus vectorsof the invention may be used for gene delivery to host cells that aretypically refractory to AAV transduction. Thus, these duplexedparvovirus vectors have a different (e.g., broader) host range than doAAV vectors.

The duplexed parvovirus vectors disclosed herein are dimericself-complementary (sc) polynucleotides (typically, DNA) packaged withina viral capsid, preferably a parvovirus capsid, more preferably, an AAVcapsid. In some respects, the viral genome that is packaged within thecapsid is essentially a “trapped” replication intermediate that cannotbe resolved to produce the plus and minus polarity parvovirus DNAstrands. Accordingly, the duplexed parvovirus vectors of the inventionappear to circumvent the need for host cell mediated synthesis ofcomplementary DNA inherent in conventional recombinant AAV (rAAV)vectors, thereby addressing one of the limitations of rAAV vectors.

This result is accomplished by allowing the virus to package essentiallydimeric inverted repeats of the single-stranded parvovirus (e.g., AAV)vector genome such that both strands, joined at one end, are containedwithin a single infectious capsid. Upon release from the capsid, thecomplementary sequences re-anneal to form transcriptionally activedouble-stranded DNA within the target cell.

The duplexed parvovirus vectors disclosed herein are fundamentallydifferent from conventional parvovirus (e.g., rAAV) vectors, and fromthe parent parvovirus (e.g., AAV), in that the vDNA may form adouble-stranded hairpin structure due to intrastrand base pairing, andthat both DNA strands are encapsidated. Thus, the duplexed parvovirusvector is functionally similar to double-stranded DNA virus vectorsrather than the parvovirus from which it was derived. This featureaddresses a previously recognized shortcoming of rAAV mediated genetransfer, which is the limited propensity of the desired target cell tosynthesize complementary DNA to the single-stranded genome normallyencapsidated by the Parvoviridae.

The viral capsid may be from any parvovirus, either an autonomousparvovirus or dependovirus, as described above. Preferably, the viralcapsid is an AAV capsid (e.g., AAV1, AAV2, AAV3, AAV4, AAV5 or AAV6capsid). In general, the AAV1 capsid, AAV5 capsid, and AAV3 capsid arepreferred. The choice of parvovirus capsid may be based on a number ofconsiderations as known in the art, e.g., the target cell type, thedesired level of expression, the nature of the heterologous nucleotidesequence to be expressed, issues related to viral production, and thelike. For example, the AAV1 capsid may be advantageously employed forskeletal muscle, liver and cells of the central nervous system (e.g.,brain); AAV5 for cells in the airway and lung; AAV3 for bone marrowcells; and AAV4 for particular cells in the brain (e.g., appendablecells).

The parvovirus particle may be a “hybrid” particle in which the viralTRs and viral capsid are from different parvoviruses. Preferably, theviral TRs and capsid are from different serotypes of AAV (e.g., asdescribed in international patent publication WO 00/28004, U.S.provisional application No. 60/248,920; and Chao et al., (2000)Molecular Therapy 2:619; the disclosures of which are incorporatedherein in their entireties. Likewise, the parvovirus may have a“chimeric” capsid (e.g., containing sequences from differentparvoviruses) or a “targeted” capsid (e.g., a directed tropism) asdescribed in these publications.

As used herein, a “duplexed parvovirus particle” encompasses hybrid,chimeric and targeted virus particles. Preferably, the duplexedparvovirus particle has an AAV capsid, which may further by a chimericor targeted capsid, as described above.

A duplexed parvovirus vector according to the invention may be producedby any suitable method. Preferably, the template for producing the vDNAis one that preferentially gives rise to a duplexed, rather thanmonomeric vDNA (i.e., the majority of vDNA produced are duplexed) whichhas the capacity to form a double-stranded vDNA. Preferably, at leastabout 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or more of the replicationproducts from the template are duplexed.

In one particular embodiment, the template is a DNA molecule comprisingone or more terminal repeat (TR) sequences. The template also comprisesa modified TR that cannot be resolved (i.e., nicked) by the parvovirusRep proteins. During replication, the inability of Rep protein toresolve the modified TR will result in a stable intermediate with thetwo “monomers” covalently attached by the non-resolvable TR. This“duplexed” molecule may be packaged within the parvovirus (AAV) capsidto produce a novel duplexed parvovirus vector.

While not wishing to be held to any particular theory of the invention,it is likely that the virion genome is retained in a single-strandedform while packaged within the viral capsid. Upon release from thecapsid during viral infection, it appears that the dimeric molecule“snaps back” or anneals to form a double-stranded molecule byintra-strand basepairing, with the non-resolvable TR sequence forming acovalently-closed hairpin structure at one end. This double-strandedvDNA obviates host cell mediated second-strand synthesis, which has beenpostulated to be a rate-limiting step for AAV transduction.

In preferred embodiments, the template further comprises a heterologousnucleotide sequence(s) (as described below) to be packaged for deliveryto a target cell. According to this particular embodiment, theheterologous nucleotide sequence is located between the viral TRs ateither end of the substrate. In further preferred embodiments, theparvovirus (e.g., AAV) cap genes and parvovirus (e.g., AAV) rep genesare deleted from the template (and the vDNA produced therefrom). Thisconfiguration maximizes the size of the heterologous nucleic acidsequence(s) that can be carried by the parvovirus capsid.

In one particular embodiment, the template for producing the inventiveduplexed parvovirus vectors contains at least one TR at the 5′ and 3′ends, flanking a heterologous nucleotide sequence of interest (asdescribed below). The TR at one end of the substrate is non-resolvable,i.e., it cannot be resolved (nicked) by Rep protein. During replication,the inability of Rep protein to resolve one of the TRs will result in astable intermediate with the two “monomers” covalently attached by thenon-functional (i.e., non-resolvable) TR. The heterologous nucleotidesequence may be in either orientation with respect to the non-resolvableTR.

The term “flanked” is not intended to indicate that the sequences arenecessarily contiguous. For example, in the example in the previousparagraph, there may be intervening sequences between the heterologousnucleotide sequence and the TR. A sequence that is “flanked” by twoother elements, indicates that one element is located 5′ to the sequenceand the other is located 3′ to the sequence; however, there may beintervening sequences therebetween.

According to this embodiment, the template for producing the duplexedparvovirus vDNA of the invention is preferably about half of the size ofthe wild-type parvovirus genome (e.g., AAV) corresponding to the capsidinto which the vDNA will be packaged. Alternatively, stated, thetemplate is preferably from about 40% to about 55% of wt, morepreferably from about 45% to about 52% of wt. Thus, the duplexed vDNAproduced from this template will preferably have a total size that isapproximately the size of the wild-type parvovirus genome (e.g., AAV)corresponding to the capsid into which the vDNA will be packaged, e.g.,from about 80% to about 105% of wt. In the case of AAV, it is well-knownin the art that the AAV capsid disfavors packaging of vDNA thatsubstantially deviate in size from the wt AAV genome. In the case of anAAV capsid, the duplexed vDNA is preferably approximately 5.2 kb in sizeor less. In other embodiments, the duplexed vDNA is preferably greaterthan about 3.6, 3.8, 4.0, 4.2, or 4.4 kb in length and/or less thanabout 5.4, 5.2, 5.0 or 4.8 kb in length.

Alternatively stated, the heterologous nucleotide sequence(s) willtypically be less than about 2.5 kb in length (more preferably less thanabout 2.4 kb, still more preferably less than about 2.2 kb in length,yet more preferably less than about 2.1 kb in length) to facilitatepackaging of the duplexed template by the parvovirus (e.g., AAV) capsid.

In another particular embodiment, the template itself is duplexed, i.e.,is a dimeric self-complementary molecule. According to this embodiment,the template comprises a resolvable TR at either end. The templatefurther comprises a centrally-located non-resolvable TR (as describedabove). In other words, each half of the template on either side of thenon-resolvable TR is approximately the same length. Each half of thetemplate (i.e., between the resolvable and non-resolvable TR) comprisesone or more heterologous nucleotide sequence(s) of interest. Theheterologous nucleotide sequence(s) in each half of the molecule isflanked by a resolvable TR and the central non-resolvable TR.

The sequences in either half of the template are substantiallycomplementary (i.e., at least about 90%, 95%, 98%, 99% nucleotidesequence complementarity or more), so that the replication products fromthe template may form double-stranded molecules due to base-pairingbetween the complementary sequences. In other words, the template isessentially an inverted repeat with the two halves joined by thenon-resolvable TR.

Preferably, the heterologous nucleotide sequence(s) in each half of thetemplate are essentially completely self-complementary (i.e., containsan insignificant number of mis-matched bases, or even no mismatchedbases). It is also preferred that the two halves of the nucleotidesequence are essentially completely self-complementary.

According to this embodiment, the template (and the vDNA producedtherefrom) is preferably approximately the same size as the wt genomenaturally encapsulated by the parvovirus capsid (e.g., AAV), i.e., tofacilitate efficient packaging into the parvovirus capsid. For example,in the case of an AAV capsid, the template is preferably approximatelythe size of the wt AAV genome. In particular embodiments, the templateis approximately 5.2 kb in size or less. In other embodiments, thetemplate is preferably greater than about 3.6, 3.8, 4.0, 4.2, or 4.4 kbin length and/or less than about 5.4, 5.2, 5.0 or 4.8 kb in length. Asan alternative statement, the template is preferably in the range of 80%to 105% of the wildtype parvovirus genome (e.g., AAV).

The TR(s) (resolvable and non-resolvable) are preferably AAV sequences,with serotypes 1, 2, 3, 4, 5 and 6 being preferred. The term “terminalrepeat” includes synthetic sequences that function as an AAV invertedterminal repeat, such as the “double-D sequence” as described in U.S.Pat. No. 5,478,745 to Samulski et al., the disclosure of which isincorporated in its entirety herein by reference. Resolvable AAV TRsaccording to the present invention need not have a wild-type TR sequence(e.g., a wild-type sequence may be altered by insertion, deletion,truncation or missense mutations), as long as the TR mediates thedesired functions, e.g., virus packaging, integration, and/or provirusrescue, and the like. Typically, but not necessarily, the TRs are fromthe same parvovirus, e.g., both TR sequences are from AAV2.

Those skilled in the art will appreciate that the viral Rep protein(s)used for producing the inventive duplexed vectors are selected withconsideration for the source of the viral TRs. For example, the AAV5 TRinteracts more efficiently with the AAV5 Rep protein.

The genomic sequences of the various autonomous parvoviruses and thedifferent serotypes of AAV, as well as the sequences of the TRs, capsidsubunits, and Rep proteins are known in the art. Such sequences may befound in the literature or in public databases such as GenBank. See,e.g., GenBank Accession Numbers NC 002077, NC 001863, NC 001862, NC001829, NC 001729, NC 001701, NC 001510, NC 001401, AF063497, U89790,AF043303, AF028705, AF028704, J02275, J01901, J02275, X01457, AF288061,AH009962, AY028226, AY028223, NC 001358, NC 001540; the disclosures ofwhich are incorporated herein in their entirety. See also, e.g.,Chiorini et al., (1999) J. Virology 73:1309; Xiao et al., (1999) J.Virology 73:3994; Muramatsu et al., (1996) Virology 221:208;international patent publications WO 00/28061, WO 99/61601, WO 98/11244;U.S. Pat. No. 6,156,303; the disclosures of which are incorporatedherein in their entirety. An early description of the AAV1, AAV2 andAAV3 TR sequences is provided by Xiao, X., (1996), “Characterization ofAdeno-associated virus (AAV) DNA replication and integration,” Ph.D.Dissertation, University of Pittsburgh, Pittsburgh, Pa. (incorporatedherein it its entirety).

The non-resolvable TR may be produced by any method known in the art.For example, insertion into the TR will displace the nicking site (i.e.,trs) and result in a non-resolvable TR. The designation of the variousregions or elements within the TR are known in the art. An illustrationof the regions within the AAV TR is provided in FIG. 6 (see also,BERNARD N. FIELDS et al., VIROLOGY, volume 2, chapter 69, FIG. 5, 3ded., Lippincott-Raven Publishers). The insertion is preferably made intothe sequence of the terminal resolution site (trs). Alternatively, theinsertion may be made at a site between the Rep Binding Element (RBE)within the A element and the trs, which is adjacent to the D element(see FIG. 6). The core sequence of the AAV trs site is known in the artand has been described by Snyder et al., (1990) Cell 60:105; Snyder etal., (1993) J. Virology 67:6096; Brister & Muzyczka, (2000) J. Virology74:7762; Brister & Muzyczka, (1999) J. Virology 73:9325 (the disclosuresof which are hereby incorporated by reference in their entireties). Forexample, Brister & Muzyczka, (1999) J. Virology 73:9325 describes a coretrs sequence of 3′-CCGGT/TG-5′ adjacent to the D element. Snyder et al.,(1993) J. Virology 67:6096 identified the minimum trs sequence as3′-GGT/TGA-5′, which substantially overlaps the sequence identified byBrister & Muzyczka.

Preferably, the insertion is in the region of the trs site. Theinsertion may be of any suitable length that will reduce orsubstantially eliminate (e.g., by 60%, 70%, 80%, 90%, 95% or greater)resolution of the TR. Preferably, the insertion is at least about 3, 4,5, 6, 10, 15, 20 or 30 nucleotides or more. There are no particularupper limits to the size of the inserted sequence, as long as suitablelevels of viral replication and packaging are achieved (e.g., theinsertion can be as long as 50, 100, 200 or 500 nucleotides or longer).

In another preferred embodiment, the TR may be rendered non-resolvableby deletion of the trs site. The deletions may extend 1, 3, 5, 8, 10,15, 20, 30 nucleotides or more beyond the trs site, as long as thetemplate retains the desired functions. In addition to the trs site,some or all of the D element may be deleted. Deletions may furtherextend into the A element, however those skilled in the art willappreciate that it may be advantageous to retain the RBE in the Aelement, e.g., to facilitate efficient packaging. Deletions into the Aelement may be 2, 3, 4, 5, 8, 10, or 15 nucleotides in length or more,as long as the non-resolvable TR retains any other desired functions. Itis further preferred that some or all of the parvovirus (e.g., AAV)sequences going beyond the D element outside the TR sequence (e.g., tothe right of the D element in FIG. 6) be deleted to prevent geneconversion to correct the altered TR.

As still a further alternative, the sequence at the nicking site may bemutated so that resolution by Rep protein is reduced or substantiallyeliminated. For example, A and/or C bases may be substituted for Gand/or T bases at or near the nicking site. The effects of substitutionsat the terminal resolution site on Rep cleavage have been described byBrister & Muzyczka, (1999) J. Virology 73:9325 (the disclosure of whichis hereby incorporated by reference). As a further alternative,nucleotide substitutions in the regions surrounding the nicking site,which have been postulated to form a stem-loop structure, may also beused to reduce Rep cleavage at the terminal resolution site (Id.).

Those skilled in the art will appreciate that the alterations in thenon-resolvable TR may be selected so as to maintain desired functions,if any, of the altered TR (e.g., packaging, Rep recognition,site-specific integration, and the like).

In more preferred embodiments, the TR will be resistant to the processof gene conversion as described by Samulski et al., (1983) Cell 33:135.Gene conversion at the non-resolvable TR will restore the trs site,which will generate a resolvable TR and result in an increase in thefrequency of monomeric replication products. Gene conversion results byhomologous recombination between the resolvable TR and the altered TR.

One strategy to reduce gene conversion is to produce virus using a cellline (preferably, mammalian) that is defective for DNA repair, as knownin the art, as these cell lines will be impaired in their ability tocorrect the mutations introduced into the viral template.

Alternatively, templates that have a substantially reduced rate of geneconversion can be generated by introducing a region of non-homology intothe non-resolvable TR. Non-homology in the region surrounding the trselement between the non-resolvable TR and the unaltered TR on thetemplate will reduce or even substantially eliminate gene conversion.

Any suitable insertion or deletion may be introduced into thenon-resolvable TR to generate a region of non-homology, as long as geneconversion is reduced or substantially eliminated. Strategies thatemploy deletions to create non-homology are preferred. It is furtherpreferred that the deletion does not unduly impair replication andpackaging of the template. In the case of a deletion, the same deletionmay suffice to impair resolution of the trs site as well as to reducegene conversion.

As a further alternative, gene conversion may be reduced by insertionsinto the non-resolvable TR or, alternatively, into the A element betweenthe RBE and the trs site. The insertion is typically at least about 3,4, 5, 6, 10, 15, 20 or 30 nucleotides or more nucleotides in length.There is no particular upper limit to the size of the inserted sequence,which may be as long as 50, 100, 200 or 500 nucleotides or longer,however, it is preferred that the insertion does not unduly impairreplication and packaging of the template.

In alternative embodiments, the non-resolvable TR may be anaturally-occurring TR (or altered form thereof) that is non-resolvableunder the conditions used. For example, the non-resolvable TR may not berecognized by the Rep proteins used to produce the vDNA from thetemplate. To illustrate, the non-resolvable TR may be an autonomousparvovirus sequence that is not recognized by AAV Rep proteins. As ananother illustrative example, the resolvable TR and Rep proteins may befrom one AAV serotype (e.g., AAV2), and the non-resolvable TR will befrom another AAV serotype (e.g., AAV5) that is not recognized by theAAV2 Rep proteins.

As a yet further alternative, the non-resolvable sequence may be anyinverted repeat sequence that forms a hairpin structure and cannot becleaved by the Rep proteins.

As still a further alternative, a half-genome size template may be usedto produce a parvovirus particle carrying a duplexed vDNA, produced froma half-genome sized template, as described in the Examples herein and byHirata & Russell, (2000) J. Virology 74:4612. This report describespackaging of paired monomers and transient RF intermediates when AAVgenomes were reduced to less than half-size of the wtAAV genome (<2.5kb). These investigators found that monomeric genomes were the preferredsubstrate for gene correction by homologous recombination, and thatduplexed genomes functioned less well than did monomeric genomes in thisassay. This report did not investigate or suggest the use of duplexedgenomes as vectors for gene delivery.

Preferably, according to this embodiment, the template will beapproximately one-half of the size of the vDNA that can be packaged bythe parvovirus capsid. For example, for an AAV capsid, the template ispreferably approximately one-half of the wt AAV genome in length, asdescribed above.

The template (as described above) is replicated to produce a duplexedvector genome (vDNA) of the invention, which is capable of forming adouble-stranded DNA under appropriate conditions. The duplexed moleculeis substantially self-complementary so as to be capable of forming adouble-stranded viral DNA (i.e., at least 90%, 95%, 98%, 99% nucleotidesequence complementarity or more). Base-pairing between individualnucleotide bases or polynucleotide sequences is well-understood in theart. Preferably, the duplexed parvovirus viral DNA is essentiallycompletely self-complementary (i.e., contains no or an insignificantnumber of mis-matched bases). In particular, it is preferred that theheterologous nucleotide sequence(s) (e.g., the sequences to betranscribed by the cell) are essentially completely self-complementary.

In general, the duplexed parvoviruses may contain non-complementarity tothe extent that expression of the heterologous nucleotide sequence(s)from the duplexed parvovirus vector is more efficient than from acorresponding monomeric vector.

The duplexed parvoviruses of the present invention provide the host cellwith a double-stranded molecule that addresses one of the drawbacks ofrAAV vectors, i.e., the need for the host cell to convert thesingle-stranded rAAV vDNA into a double-stranded DNA. The presence ofany substantial regions of non-complementarity within the virion DNA, inparticular, within the heterologous nucleotide sequence(s) will likelybe recognized by the host cell, and will result in DNA repair mechanismsbeing recruited to correct the mismatched bases, thereby counteractingthe advantageous characteristics of the duplexed parvovirus vectors,e.g., the inventive vectors reduce or eliminate the need for the hostcell to process the viral template.

Production of Duplexed Parvovirus Vectors.

In general, methods of producing AAV vectors are applicable to producingthe duplexed parvovirus vectors of the invention; the primary differencebetween the methods is the structure of the template or substrate to bepackaged. To produce a duplexed parvovirus vector according to thepresent invention, a template as described above will be used to producethe encapsidated viral genome.

The template described above is preferably a DNA substrate and may beprovided in any form known in the art, including but not limited to aplasmid, naked DNA vector, bacterial artificial chromosome (BAC), yeastartificial chromosome (YAC) or a viral vector (e.g., adenovirus,herpesvirus, Epstein-Barr Virus, AAV, baculoviral, retroviral vectors,and the like). Alternatively, the template may be stably incorporatedinto the genome of a packaging cell.

In one particular embodiment, the inventive parvovirus vectors may carryduplexed half-genome sized monomeric vDNA as described in the Examplesherein. This means of providing cells with a duplexed parvovirus (e.g.,AAV) virion DNA takes advantage of the rolling-hairpin mode ofreplication in which monomeric vDNA is generated from dimeric invertedrepeat intermediates (Cavalier-Smith et al.,. (1974) Nature 250:467;Straus et al., (1976) Proc. Nat. Acad. Sci. USA 73:742). When the genomeis sufficiently small, the dimeric inverted repeats themselves can beencapsidated into the virion. This approach will generate a mixedpopulation of monomeric and dimeric molecules. The duplexed parvovirusvectors may be isolated by known techniques, e.g., separation over acesium chloride density gradient.

Duplexed parvovirus particles according to the invention may be producedby any method known in the art, e.g., by introducing the template to bereplicated and packaged into a permissive or packaging cell, as thoseterms are understood in the art (e.g., a “permissive” cell can beinfected or transduced by the virus; a “packaging” cell is a stablytransformed cell providing helper functions).

In one embodiment, a method is provided for producing a duplexedparvovirus particle, comprising: providing to a cell permissive forparvovirus replication (a) a nucleotide sequence encoding a template forproducing vector genome of the invention (as described in detail above);(b) nucleotide sequences sufficient for replication of the template toproduce a vector genome; (c) nucleotide sequences sufficient to packagethe vector genome into a parvovirus capsid, under conditions sufficientfor replication and packaging of the vector genome into the parvoviruscapsid, whereby duplexed parvovirus particles comprising the vectorgenome encapsidated within the parvovirus capsid are produced in thecell. Preferably, the parvovirus replication and/or capsid codingsequences are AAV sequences.

Any method of introducing the nucleotide sequence carrying the templateinto a cellular host for replication and packaging may be employed,including but not limited to, electroporation, calcium phosphateprecipitation, microinjection, cationic or anionic liposomes, andliposomes in combination with a nuclear localization signal. Inembodiments wherein the template is provided by a virus vector, standardmethods for producing viral infection may be used.

Any suitable permissive or packaging cell known in the art may beemployed to produce the duplexed vectors. Mammalian cells are preferred.Also preferred are trans-complementing packaging cell lines that providefunctions deleted from a replication-defective helper virus, e.g., 293cells or other E1a trans-complementing cells. Also preferred aremammalian cells or cell lines that are defective for DNA repair as knownin the art, as these cell lines will be impaired in their ability tocorrect the mutations introduced into the viral template.

The template may contain some or all of the parvovirus (e.g., AAV) capand rep genes. Preferably, however, some or all of the cap and repfunctions are provided in trans by introducing a packaging vector(s)encoding the capsid and/or Rep proteins into the cell. Most preferably,the template does not encode the capsid or Rep proteins. Alternatively,a packaging cell line is used that is stably transformed to express thecap and/or rep genes (see, e.g., Gao et al., (1998) Human Gene Therapy9:2353; Inoue et al., (1998) J. Virol. 72:7024; U.S. Pat. No. 5,837,484;WO 98/27207; U.S. Pat. No. 5,658,785; WO 96/17947).

In addition, helper virus functions are preferably provided for thevector to propagate new virus particles. Both adenovirus and herpessimplex virus may serve as helper viruses for AAV. See, e.g., BERNARD N.FIELDS et al., VIROLOGY, volume 2, chapter 69 (3d ed., Lippincott-RavenPublishers). Exemplary helper viruses include, but are not limited to,Herpes simplex (HSV) varicella zoster, cytomegalovirus, and Epstein-Barrvirus. The multiplicity of infection (MOI) and the duration of theinfection will depend on the type of virus used and the packaging cellline employed. Any suitable helper vector may be employed. Preferably,the helper vector(s) is a plasmid, for example, as described by Xiao etal., (1998) J. Virology 72:2224. The vector can be introduced into thepackaging cell by any suitable method known in the art, as describedabove.

In one method, the inventive duplexed parvovirus vectors may be producedby co-transfection of a rep/cap vector encoding AAV packaging functionsand the template encoding the AAV vDNA into human cells infected withadenovirus (Samulski et al., (1989) J. Virology 63:3822). Underoptimized conditions, this procedure can yield up to 10⁹ infectiousunits of virus particles per ml. One drawback of this method, however,is that it results in the co-production of contaminating wild-typeadenovirus. Since several adenovirus proteins (e.g., fiber, hexon, etc.)are known to produce a cytotoxic T-lymphocyte (CTL) immune response inhumans (Yang and Wilson, (1995) J. Immunol. 155:2564; Yang et al.,(1995) J. Virology 69:2004; Yang et al., (1994) Proc. Nat. Acad. Sci.USA 91:4407), this represents a significant drawback when using theserAAV preparations (Monahan et al., (1998) Gene Therapy 5:40).

Vector stocks free of contaminating helper virus may be obtained by anymethod known in the art. For example, duplexed virus and helper virusmay be readily differentiated based on size. The duplexed virus may alsobe separated away from helper virus based on affinity for a heparinsubstrate (Zolotukhin et al. (1999) Gene Therapy 6:973). Preferably,deleted replication-defective helper viruses are used so that anycontaminating helper virus is not replication competent. As a furtheralternative, an adenovirus helper lacking late gene expression may beemployed, as only adenovirus early gene expression is required tomediate packaging of the duplexed virus. Adenovirus mutants defectivefor late gene expression are known in the art (e.g., ts100K and ts149adenovirus mutants).

A preferred method for providing helper functions employs anon-infectious adenovirus miniplasmid that carries all of the helpergenes required for efficient AAV production (Ferrari et al., (1997)Nature Med. 3:1295; Xiao et al., (1998) J. Virology 72:2224). The rAAVtiters obtained with adenovirus miniplasmids are forty-fold higher thanthose obtained with conventional methods of wild-type adenovirusinfection (Xiao et al., (1998) J. Virology 72:2224). This approachobviates the need to perform co-transfections with adenovirus (Holscheret al., (1994), J. Virology 68:7169; Clark et al., (1995) Hum. GeneTher. 6:1329; Trempe and Yang, (1993), in, Fifth Parvovirus Workshop,Crystal River, Fla.).

Other methods of producing rAAV stocks have been described, includingbut not limited to, methods that split the rep and cap genes ontoseparate expression cassettes to prevent the generation ofreplication-competent AAV (see, e.g., Allen et al., (1997) J. Virol.71:6816), methods employing packaging cell lines (see, e.g., Gao et al.,(1998) Human Gene Therapy 9:2353; Inoue et al., (1998) J. Virol.72:7024; U.S. Pat. No. 5,837,484; WO 98/27207; U.S. Pat. No. 5,658,785;WO 96/17947), and other helper virus free systems (see, e.g., U.S. Pat.No. 5,945,335 to Colosi).

Herpesvirus may also be used as a helper virus in AAV packaging methods.Hybrid herpesviruses encoding the AAV Rep protein(s) may advantageouslyfacilitate for more scalable AAV vector production schemes. A hybridherpes simples virus type I (HSV-1) vector expressing the AAV-2 rep andcap genes has been described (Conway et al., (1999) Gene Therapy 6:986and WO 00/17377, the disclosures of which are incorporated herein intheir entireties).

In sum, the viral template to be replicated and packaged, parvovirus capgenes, appropriate parvovirus rep genes, and (preferably) helperfunctions are provided to a cell (e.g., a permissive or packaging cell)to produce parvovirus particles carrying the duplexed genome (i.e., thegenome is capable of forming a “snap back” or self-complementary DNAafter viral uncoating). The combined expression of the rep and cap genesencoded by the template and/or the packaging vector(s) and/or the stablytransformed packaging cell results in the production of a parvovirusparticle in which a parvovirus capsid packages a duplexed parvovirusgenome according to the invention. The duplexed parvovirus particles areallowed to assemble within the cell, and may then be recovered by anymethod known by those of skill in the art.

Alternatively, in vitro packaging approaches, as are known in the art,may also be used to produce the dimeric vDNA templates described herein.To illustrate, the duplexed vDNA sequence may be amplified in bacteriausing single-stranded M13 phage. The resolvable TRs at each end of thevDNA carried by the M13 will anneal to form a double-stranded sequence,which may be cleaved with a suitable restriction enzyme to excise thedimeric vDNA from the M13 backbone. As yet a further alternative, PCR orother suitable amplification techniques may be used to amplify theduplexed vDNA sequence from a dimeric self-complementary template, asdescribed above.

The reagents and methods disclosed herein may be employed to producehigh-titer stocks of the inventive parvovirus vectors, preferably atessentially wild-type titers. It is also preferred that the parvovirusstock has a titer of at least about 10⁵ transducing units (tu)/ml, morepreferably at least about 10⁶ to/ml, more preferably at least about 10⁷tu/ml, yet more preferably at least about 10⁸ to/ml, yet more preferablyat least about 10⁹ to/ml, still yet more preferably at least about 10¹⁰to/ml, still more preferably at least about 10¹¹ to/ml, or more.

Alternatively stated, the parvovirus stock preferably has a titer of atleast about 1 tu/cell, more preferably at least about 5 tu/cell, stillmore preferably at least about 20 tu/cell, yet more preferably at leastabout 50 tu/cell, still more preferably at least about 100 tu/cell, morepreferably still at least about 250 tu/cell, most preferably at leastabout 500 tu/cell, or even more.

Further, the duplexed parvovirus vectors of the invention, may have animproved transducing unit (tu)/particle ratio over conventionalparvovirus vectors. Preferably, the tu/particle ratio is less than about50:1, less than about 20:1, less than about 15:1, less than about 10:1,less than about 8:1, less than about 7:1, less than about 6:1, less thanabout 5:1, less than about 4:1, or lower. There is no particular lowerlimit to the tu/particle ratio. Typically, the tu/particle ratio will begreater than about 1:1, 2:1, 3:1 or 4:1.

Applications of the Present Invention.

A further aspect of the invention is a method of delivering a nucleotidesequence to a cell using the duplexed parvovirus vectors describedherein. The vector may be delivered to a cell in vitro or to a subjectin vivo by any suitable method known in the art. Alternatively, thevector may be delivered to a cell ex vivo, and the cell administered toa subject, as known in the art.

The present methods may be advantageously employed to provide moreefficient transduction of target cells than wtAAV vectors. Toillustrate, the duplexed parvovirus vectors may transduce at a higherrate than wt AAV vectors. Alternatively, or additionally, the duplexedparvovirus vectors may provide for a more rapid onset of transgeneexpression, a higher level of transgene expression, and/or a longerpersistence of transgene expression than AAV vectors.

The inventive duplexed parvovirus vectors and methods may further finduse in methods of administering a nucleotide sequence to a cell that istypically non-permissive for transduction by AAV, or is onlyinefficiently transduced by AAV. Exemplary cells include but are notlimited to dendritic cells, particular types of cancer or tumor cells,astrocytes, and bone marrow stem cells. Moreover, the methods disclosedherein may be advantageously practiced with non-replicating orslowly-replicating cells that only inefficiently support second-strandAAV synthesis, such as the liver, central nervous system (e.g., brain),and particular populations of cells within muscle (e.g., fast-twitchfibers).

Accordingly, the duplexed parvovirus vectors disclosed herein may have adistinct target cell range (e.g., a broader range of target cells) ascompared with rAAV vectors. While not wishing to be held to anyparticular theory of the invention, it appears that cells that arerefractory to transduction by rAAV may be permissive for the inventiveduplexed parvovirus vectors, which provide a double-stranded molecule tothe host cell. Thus, the present invention finds use for delivering anucleotide sequence to a cell that is non-permissive for conventionalrAAV vectors or only poorly transduced by rAAV vectors because it cannotefficiently support second-strand synthesis of the viral DNA.

One of the characteristics of wtAAV vectors is the protracted lag periodbefore high level transgene expression is observed. The duplexedparvovirus vectors disclosed herein may provide a more rapid andaggressive gene delivery system than wtAAV vectors because they obviatethe step of complementary strand synthesis.

Accordingly, the inventive duplexed parvovirus vectors find use inmethods of treating cancer or tumors, e.g., by delivery of anti-canceragents or cancer antigens. In particular embodiments, the inventivemethods are used to administer anti-cancer agents or cancer antigens toprevent metastasis, e.g., following surgical removal of a primary tumor.

The inventive methods and duplexed parvovirus vectors may alsoadvantageously be used in the treatment of individuals with metabolicdisorders (e.g., ornithine transcarbamylase deficiency). Such disorderstypically require a relatively rapid onset of expression of atherapeutic polypeptide by the gene delivery vector. As still a furtheralternative, the inventive vectors may be administered to provide agentsthat improve transplant survivability (e.g., superoxide dismutase) orcombat sepsis.

Moreover, the inventors have found that dendritic cells (DC), which arerefractory to wtAAV vectors (Jooss et al., (1998) 72:4212), arepermissive for the duplexed parvovirus vectors disclosed herein.Accordingly, as yet a further aspect, the present invention providesmethods of delivering a nucleotide sequence to DC, e.g., to induce animmune response to a polypeptide encoded by the nucleotide sequence.Preferably, the nucleotide sequence encodes an antigen from aninfectious agent or a cancer antigen.

As still a further aspect, the present invention may be employed todeliver a heterologous nucleotide sequence in situations in which it isdesirable to regulate the level of transgene expression (e.g.,transgenes encoding hormones or growth factors, as described below). Themore rapid onset of transgene expression by the duplexed parvovirusvectors disclosed herein make these gene delivery vehicles more amenableto such treatment regimes than are rAAV vectors.

Any heterologous nucleotide sequence(s) (as defined above) may bedelivered according to the present invention. Nucleic acids of interestinclude nucleic acids encoding polypeptides, preferably therapeutic(e.g., for medical or veterinary uses) or immunogenic (e.g., forvaccines) polypeptides.

A “therapeutic polypeptide” is a polypeptide that may alleviate orreduce symptoms that result from an absence or defect in a protein in acell or subject.

Alternatively, a “therapeutic polypeptide” is one that otherwise confersa benefit to a subject, e.g., anti-cancer effects or improvement intransplant survivability.

Preferably, the heterologous nucleotide sequence or sequences will beless than about 2.5 kb in length (more preferably less than about 2.4kb, still more preferably less than about 2.2 kb, yet more preferablyless than about 2.0 kb in length) to facilitate packaging of theduplexed template by the parvovirus (e.g., AAV) capsid. Exemplarynucleotide sequences encode Factor IX, Factor X, lysosomal enzymes(e.g., hexosaminidase A, associated with Tay-Sachs disease, or iduronatesulfatase, associated with Hunter Syndrome/MPS II), erythropoietin,angiostatin, endostatin, superoxide dismutase, globin, leptin, catalase,tyrosine hydroxylase, as well as cytokines (e.g., α-interferon,β-interferon, interferon-γ, interleukin-2, interleukin-4, interleukin12, granulocyte-macrophage colony stimulating factor, lymphotoxin, andthe like), peptide growth factors and hormones (e.g., somatotropin,insulin, insulin-like growth factors 1 and 2, platelet derived growthfactor, epidermal growth factor, fibroblast growth factor, nerve growthfactor, neurotrophic factor-3 and -4, brain-derived neurotrophic factor,glial derived growth factor, transforming growth factor-α and -β, andthe like), receptors (e.g., tumor necrosis factor receptor). In otherexemplary embodiments, the heterologous nucleotide sequence encodes amonoclonal antibodies, preferably a single-chained monoclonal antibodyor a monoclonal antibody directed against a cancer or tumor antigen(e.g., HER2/neu, and as described below). Other illustrativeheterologous nucleotide sequences encode suicide gene products(thymidine kinase, cytosine deaminase, diphtheria toxin, cytochromeP450, deoxycytidine kinase, and tumor necrosis factor), proteinsconferring resistance to a drug used in cancer therapy, and tumorsuppressor gene products.

As a further alternative, the heterologous nucleic acid sequence mayencode a reporter polypeptide (e.g., an enzyme such as Green FluorescentProtein, alkaline phosphatase).

Alternatively, in particular embodiments of the invention, the nucleicacid of interest may encode an antisense nucleic acid, a ribozyme (e.g.,as described in U.S. Pat. No. 5,877,022), RNAs that effectspliceosome-mediated trans-splicing (see, Puttaraju et al., (1999)Nature Biotech. 17:246; U.S. Pat. Nos. 6,013,487; 6,083,702),interfering RNAs (RNAi) that mediate gene silencing (see, Sharp et al.,(2000) Science 287:2431) or other non-translated RNAs, such as “guide”RNAs (Gorman et al., (1998) Proc. Nat. Acad. Sci. USA 95:4929; U.S. Pat.No. 5,869,248 to Yuan et al.), and the like.

The parvovirus vector may also encode a heterologous nucleotide sequencethat shares homology with and recombines with a locus on the hostchromosome. This approach may be utilized to correct a genetic defect inthe host cell.

The present invention may also be used to express an immunogenicpolypeptide in a subject, e.g., for vaccination. The nucleic acid mayencode any immunogen of interest known in the art including, but are notlimited to, immunogens from human immunodeficiency virus, influenzavirus, gag proteins, tumor antigens, cancer antigens, bacterialantigens, viral antigens, and the like.

The use of parvoviruses as vaccines is known in the art (see, e.g.,Miyamura et al. (1994) Proc. Nat. Acad. Sci USA 91:8507; U.S. Pat. No.5,916,563 to Young et al., U.S. Pat No. 5,905,040 to Mazzara et al.,U.S. Pat. Nos. 5,882,652, 5,863,541 to Samulski et al.; the disclosuresof which are incorporated herein in their entirety by reference). Theantigen may be presented in the parvovirus capsid. Alternatively, theantigen may be expressed from a heterologous nucleic acid introducedinto a recombinant vector genome. Any immunogen of interest may beprovided by the parvovirus vector. Immunogens of interest are well-knownin the art and include, but are not limited to, immunogens from humanimmunodeficiency virus, influenza virus, gag proteins, tumor antigens,cancer antigens, bacterial antigens, viral antigens, and the like.

An immunogenic polypeptide, or immunogen, may be any polypeptidesuitable for protecting the subject against a disease, including but notlimited to microbial, bacterial, protozoal, parasitic, and viraldiseases. For example, the immunogen may be an orthomyxovirus immunogen(e.g., an influenza virus immunogen, such as the influenza virushemagglutinin (HA) surface protein or the influenza virus nucleoproteingene, or an equine influenza virus immunogen), or a lentivirus immunogen(e.g., an equine infectious anemia virus immunogen, a SimianImmunodeficiency Virus (SIV) immunogen, or a Human ImmunodeficiencyVirus (HIV) immunogen, such as the HIV or SIV envelope GP160 protein,the HIV or SIV matrix/capsid proteins, and the HIV or SIV gag, pol andenv genes products). The immunogen may also be an arenavirus immunogen(e.g., Lassa fever virus immunogen, such as the Lassa fever virusnucleocapsid protein gene and the Lassa fever envelope glycoproteingene), a poxvirus immunogen (e.g., vaccinia, such as the vaccinia L1 orL8 genes), a flavivirus immunogen (e.g., a yellow fever virus immunogenor a Japanese encephalitis virus immunogen), a filovirus immunogen(e.g., an Ebola virus immunogen, or a Marburg virus immunogen, such asNP and GP genes), a bunyavirus immunogen (e.g., RVFV, CCHF, and SFSviruses), or a coronavirus immunogen (e.g., an infectious humancoronavirus immunogen, such as the human coronavirus envelopeglycoprotein gene, or a porcine transmissible gastroenteritis virusimmunogen, or an avian infectious bronchitis virus immunogen). Theimmunogen may further be a polio immunogen, herpes antigen (e.g., CMV,EBV, HSV immunogens) mumps immunogen, measles immunogen, rubellaimmunogen, diptheria toxin or other diptheria immunogen, pertussisantigen, hepatitis (e.g., hepatitis A or hepatitis B) immunogen, or anyother vaccine immunogen known in the art.

Alternatively, the immunogen may be any tumor or cancer cell antigen.Preferably, the tumor or cancer antigen is expressed on the surface ofthe cancer cell. Exemplary cancer and tumor cell antigens are describedin S. A. Rosenberg, (1999) Immunity 10:281). Other illustrative cancerand tumor antigens include, but are not limited to: BRCA1 gene product,BRCA2 gene product, gp100, tyrosinase, GAGE-1/2, BAGE, RAGE, NY-ESO-1,CDK-4, β-catenin, MUM-1, Caspase-8, KIAA0205, HPVE, SART-1, PRAME, p15,melanoma tumor antigens (Kawakami et al., (1994) Proc. Natl. Acad. Sci.USA 91:3515); Kawakami et al., (1994) J. Exp. Med., 180:347); Kawakamiet al., (1994) Cancer Res. 54:3124), including MART-1 (Coulie et al.,(1991) J. Exp. Med. 180:35), gp100 (Wick et al., (1988) J. Cutan.Pathol. 4:201) and MAGE antigen, MAGE-1, MAGE-2 and MAGE-3 (Van derBruggen et al., (1991) Science, 254:1643); CEA, TRP-1, TRP-2, P-15 andtyrosinase (Brichard et al., (1993) J. Exp. Med. 178:489); HER-2/neugene product (U.S. Pat. No. 4,968,603), CA 125, LK26, FB5 (endosialin),TAG 72, AFP, CA19-9, NSE, DU-PAN-2, CA50, SPan-1, CA72-4, HCG, STN(sialyl Tn antigen), c-erbB-2 proteins, PSA, L-CanAg, estrogen receptor,milk fat globulin, p53 tumor suppressor protein (Levine, (1993) Ann.Rev. Biochem. 62:623); mucin antigens (international patent publicationWO 90/05142); telomerases; nuclear matrix proteins; prostatic acidphosphatase; papilloma virus antigens; and antigens associated with thefollowing cancers: melanomas, metastases, adenocarcinoma, thymoma,lymphoma, sarcoma, lung cancer, liver cancer, colon cancer, non-Hodgkinslymphoma, Hodgkins lymphoma, leukemias, uterine cancer, breast cancer,prostate cancer, ovarian cancer, cervical cancer, bladder cancer, kidneycancer, pancreatic cancer and others (see, e.g., Rosenberg, (1996) Ann.Rev. Med. 47:481-91).

Alternatively, the heterologous nucleotide sequence may encode anypolypeptide that is desirably produced in a cell in vitro, ex vivo, orin vivo. For example, the inventive vectors may be introduced intocultured cells and the expressed gene product isolated therefrom.

It will be understood by those skilled in the art that the heterologousnucleotide sequence(s) of interest may be operably associated withappropriate control sequences. For example, the heterologous nucleicacid may be operably associated with expression control elements, suchas transcription/translation control signals, origins of replication,polyadenylation signals, and internal ribosome entry sites (IRES),promoters, enhancers, and the like.

Those skilled in the art will appreciate that a variety ofpromoter/enhancer elements may be used depending on the level andtissue-specific expression desired. The promoter/enhancer may beconstitutive or inducible, depending on the pattern of expressiondesired. The promoter/enhancer may be native or foreign and can be anatural or a synthetic sequence. By foreign, it is intended that thetranscriptional initiation region is not found in the wild-type hostinto which the transcriptional initiation region is introduced.

Promoter/enhancer elements that are native to the target cell or subjectto be treated are most preferred. Also preferred are promoters/enhancerelements that are native to the heterologous nucleic acid sequence. Thepromoter/enhancer element is chosen so that it will function in thetarget cell(s) of interest. Mammalian promoter/enhancer elements arealso preferred. The promoter/enhance element may be constitutive orinducible.

Inducible expression control elements are preferred in thoseapplications in which it is desirable to provide regulation overexpression of the heterologous nucleic acid sequence(s). Induciblepromoters/enhancer elements for gene delivery are preferablytissue-specific promoter/enhancer elements, and include muscle specific(including cardiac, skeletal and/or smooth muscle), neural tissuespecific (including brain-specific), liver specific, bone marrowspecific, pancreatic specific, spleen specific, retinal specific, andlung specific promoter/enhancer elements. Other induciblepromoter/enhancer elements include hormone-inducible and metal-inducibleelements. Exemplary inducible promoters/enhancer elements include, butare not limited to, a Tet on/off element, a RU486-inducible promoter, anecdysone-inducible promoter, a rapamycin-inducible promoter, and ametalothionein promoter.

In embodiments of the invention in which the heterologous nucleic acidsequence(s) will be transcribed and then translated in the target cells,specific initiation signals are generally required for efficienttranslation of inserted protein coding sequences. These exogenoustranslational control sequences, which may include the ATG initiationcodon and adjacent sequences, can be of a variety of origins, bothnatural and synthetic.

As a further advantage, the inventive duplexed parvovirus vectors may bedistinguished from rAAV vectors in that the orientation of the codingsequence with respect the resolvable TR is fixed and may be controlled.Thus, for example, the orientation and expression of the transgene maybe controlled with respect to the putative transcriptional controlelements within the resolvable TR. Moreover, control over theorientation of the transgene with respect to the non-resolvable TR mayprovide a greater level of control over the recombination productsbetween the genomes of co-infecting vectors. If either the closed end ofthe genome near the non-resolvable TR) or the open end is a preferredsubstrate for intermolecular recombination, the orientation of thecoding sequence within the recombination product can be predicted andcontrolled.

Finally, unlike rAAV vectors, the duplexed parvovirus vectors of thepresent invention are uniform in that they co-package both the plus andminus strands in a single molecule. This characteristic is desirablefrom the standpoint of producing a consistent clinical grade reagent.

Gene Transfer Technology.

The methods of the present invention also provide a means for deliveringheterologous nucleotide sequences into a broad range of cells, includingdividing and non-dividing cells. The present invention may be employedto deliver a nucleotide sequence of interest to a cell in vitro, e.g.,to produce a polypeptide in vitro or for ex vivo gene therapy. Thecells, pharmaceutical formulations, and methods of the present inventionare additionally useful in a method of delivering a nucleotide sequenceto a subject in need thereof, e.g., to express an immunogenic ortherapeutic polypeptide. In this manner, the polypeptide may thus beproduced in vivo in the subject. The subject may be in need of thepolypeptide because the subject has a deficiency of the polypeptide, orbecause the production of the polypeptide in the subject may impart sometherapeutic effect, as a method of treatment or otherwise, and asexplained further below.

In general, the present invention may be employed to deliver any foreignnucleic acid with a biological effect to treat or ameliorate thesymptoms associated with any disorder related to gene expression.Illustrative disease states include, but are not limited to: cysticfibrosis (and other diseases of the lung), hemophilia A, hemophilia B,thalassemia, anemia and other blood disorders, AIDs, Alzheimer'sdisease, Parkinson's disease, Huntington's disease, amyotrophic lateralsclerosis, epilepsy, and other neurological disorders, cancer, diabetesmellitus, muscular dystrophies (e.g., Duchenne, Becker), Gaucher'sdisease, Hurler's disease, adenosine deaminase deficiency, glycogenstorage diseases and other metabolic defects, retinal degenerativediseases (and other diseases of the eye), diseases of solid organs(e.g., brain, liver, kidney, heart), and the like.

Gene transfer has substantial potential use in understanding andproviding therapy for disease states. There are a number of inheriteddiseases in which defective genes are known and have been cloned. Ingeneral, the above disease states fall into two classes: deficiencystates, usually of enzymes, which are generally inherited in a recessivemanner, and unbalanced states, which may involve regulatory orstructural proteins, and which are typically inherited in a dominantmanner. For deficiency state diseases, gene transfer could be used tobring a normal gene into affected tissues for replacement therapy, aswell as to create animal models for the disease using antisensemutations. For unbalanced disease states, gene transfer could be used tocreate a disease state in a model system, which could then be used inefforts to counteract the disease state. Thus the methods of the presentinvention permit the treatment of genetic diseases. As used herein, adisease state is treated by partially or wholly remedying the deficiencyor imbalance that causes the disease or makes it more severe. The use ofsite-specific recombination of nucleic sequences to cause mutations orto correct defects is also possible.

The instant invention may also be employed to provide an antisensenucleic acid to a cell in vitro or in vivo. Expression of the antisensenucleic acid in the target cell diminishes expression of a particularprotein by the cell. Accordingly, antisense nucleic acids may beadministered to decrease expression of a particular protein in a subjectin need thereof. Antisense nucleic acids may also be administered tocells in vitro to regulate cell physiology, e.g., to optimize cell ortissue culture systems.

Finally, the instant invention finds further use in diagnostic andscreening methods, whereby a gene of interest is transiently or stablyexpressed in a cell culture system, or alternatively, a transgenicanimal model.

In general, the present invention can be employed to deliver anyheterologous nucleic acid to a cell in vitro, ex vivo, or in vivo.

Subjects, Pharmaceutical Formulations, Vaccines, and Modes ofAdministration.

The present invention finds use in both veterinary and medicalapplications. Suitable subjects for ex vivo gene delivery methods asdescribed above include both avians and mammals, with mammals beingpreferred. The term “avian” as used herein includes, but is not limitedto, chickens, ducks, geese, quail, turkeys and pheasants. The term“mammal” as used herein includes, but is not limited to, humans,bovines, ovines, caprines, equines, felines, canines, lagomorphs, etc.Human subjects are most preferred. Human subjects include neonates,infants, juveniles, and adults.

In particular embodiments, the present invention provides apharmaceutical composition comprising a virus particle of the inventionin a pharmaceutically-acceptable carrier and/or other medicinal agents,pharmaceutical agents, carriers, adjuvants, diluents, etc. Forinjection, the carrier will typically be a liquid. For other methods ofadministration, the carrier may be either solid or liquid. Forinhalation administration, the carrier will be respirable, and willpreferably be in solid or liquid particulate form. As an injectionmedium, it is preferred to use water that contains the additives usualfor injection solutions, such as stabilizing agents, salts or saline,and/or buffers.

In general, a “physiologically acceptable carrier” is one that is nottoxic or unduly detrimental to cells. Exemplary physiologicallyacceptable carriers include sterile, pyrogen-free water and sterile,pyrogen-free, phosphate buffered saline. Physiologically-acceptablecarriers include pharmaceutically-acceptable carriers.

By “pharmaceutically acceptable” it is meant a material that is notbiologically or otherwise undesirable, i.e., the material may beadministered to a subject without causing any undesirable biologicaleffects. Thus, such a pharmaceutical composition may be used, forexample, in transfection of a cell ex vivo or in administering a viralparticle or cell directly to a subject.

The parvovirus vectors of the invention maybe administered to elicit animmunogenic response (e.g., as a vaccine). Typically, vaccines of thepresent invention comprise an immunogenic amount of infectious virusparticles as disclosed herein in combination with apharmaceutically-acceptable carrier. An “immunogenic amount” is anamount of the infectious virus particles that is sufficient to evoke animmune response in the subject to which the pharmaceutical formulationis administered. Typically, an amount of about 10³ to about 10¹⁵ virusparticles, preferably about 10⁴ to about 10¹³, and more preferably about10⁴ to 10⁶ virus particles per dose is suitable, depending upon the ageand species of the subject being treated, and the immunogen againstwhich the immune response is desired. Subjects and immunogens are asdescribed above.

The present invention further provides a method of delivering a nucleicacid to a cell. Typically, for in vitro methods, the virus may beintroduced into the cell by standard viral transduction methods, as areknown in the art. Preferably, the virus particles are added to the cellsat the appropriate multiplicity of infection according to standardtransduction methods appropriate for the particular target cells. Titersof virus to administer can vary, depending upon the target cell type andthe particular virus vector, and may be determined by those of skill inthe art without undue experimentation.

Recombinant virus vectors are preferably administered to the cell in abiologically-effective amount. A “biologically-effective” amount of thevirus vector is an amount that is sufficient to result in infection (ortransduction) and expression of the heterologous nucleic acid sequencein the cell. If the virus is administered to a cell in vivo (e.g., thevirus is administered to a subject as described below), a“biologically-effective” amount of the virus vector is an amount that issufficient to result in transduction and expression of the heterologousnucleic acid sequence in a target cell.

The cell to be administered the inventive virus vector may be of anytype, including but not limited to neural cells (including cells of theperipheral and central nervous systems, in particular, brain cells),lung cells, retinal cells, epithelial cells (e.g., gut and respiratoryepithelial cells), muscle cells, dendritic cells, pancreatic cells(including islet cells), hepatic cells, myocardial cells, bone cells(e.g., bone marrow stem cells), hematopoietic stem cells, spleen cells,keratinocytes, fibroblasts, endothelial cells, prostate cells, germcells, and the like. Alternatively, the cell may be any progenitor cell.As a further alternative, the cell can be a stem cell (e.g., neural stemcell, liver stem cell). As still a further alternative, the cell may bea cancer or tumor cell. Moreover, the cells can be from any species oforigin, as indicated above.

In particular embodiments of the invention, cells are removed from asubject, the parvovirus vector is introduced therein, and the cells arethen replaced back into the subject. Methods of removing cells fromsubject for treatment ex vivo, followed by introduction back into thesubject are known in the art (see, e.g., U.S. Pat. No. 5,399,346; thedisclosure of which is incorporated herein in its entirety).Alternatively, the rAAV vector is introduced into cells from anothersubject, into cultured cells, or into cells from any other suitablesource, and the cells are administered to a subject in need thereof.

Suitable cells for ex vivo gene therapy are as described above.

The cells transduced with the inventive vector are preferablyadministered to the subject in a “therapeutically-effective amount” incombination with a pharmaceutical carrier. A “therapeutically-effective”amount as used herein is an amount that provides sufficient expressionof the heterologous nucleotide sequence delivered by the vector toprovide some improvement or benefit to the subject. Alternativelystated, a “therapeutically-effective” amount is an amount that willprovide some alleviation, mitigation, or decrease in at least oneclinical symptom in the subject. Those skilled in the art willappreciate that the therapeutic effects need not be complete orcurative, as long as some benefit is provided to the subject.

In alternate embodiments, cells that have been transduced with a vectoraccording to the invention may be administered to elicit an immunogenicresponse against the delivered polypeptide. Typically, a quantity ofcells expressing an immunogenic amount of the polypeptide in combinationwith a pharmaceutically-acceptable carrier is administered. An“immunogenic amount” is an amount of the expressed polypeptide that issufficient to evoke an active immune response in the subject to whichthe pharmaceutical formulation is administered. The degree of protectionconferred by the active immune response need not be complete orpermanent, as long as the benefits of administering the immunogenicpolypeptide outweigh any disadvantages thereof.

Dosages of the cells to administer to a subject will vary upon the age,condition and species of the subject, the type of cell, the nucleic acidbeing expressed by the cell, the mode of administration, and the like.Typically, at least about 10² to about 10⁸, preferably about 10³ toabout 10⁶ cells, will be administered per dose. Preferably, the cellswill be administered in a “therapeutically-effective amount”.

A further aspect of the invention is a method of treating subjects invivo with the inventive virus particles. Administration of theparvovirus particles of the present invention to a human subject or ananimal in need thereof can be by any means known in the art foradministering virus vectors.

Exemplary modes of administration include oral, rectal, transmucosal,topical, transdermal, inhalation, parenteral (e.g., intravenous,subcutaneous, intradermal, intramuscular, and intraarticular)administration, and the like, as well as direct tissue or organinjection, alternatively, intrathecal, direct intramuscular,intraventricular, intravenous, intraperitoneal, intranasal, orintraocular injections. Injectables can be prepared in conventionalforms, either as liquid solutions or suspensions, solid forms suitablefor solution or suspension in liquid prior to injection, or asemulsions. Alternatively, one may administer the virus in a local ratherthan systemic manner, for example, in a depot or sustained-releaseformulation.

The parvovirus vector administered to the subject may transduce anypermissive cell or tissue. Suitable cells for transduction by theinventive parvovirus vectors are as described above.

In particularly preferred embodiments of the invention, the nucleotidesequence of interest is delivered to the liver of the subject.Administration to the liver may be achieved by any method known in theart, including, but not limited to intravenous administration,intraportal administration, intrabiliary administration, intra-arterialadministration, and direct injection into the liver parenchyma.

In other preferred embodiments, the inventive parvovirus particles areadministered intramuscularly, more preferably by intramuscular injectionor by local administration (as defined above). Delivery to the brain isalso preferred. In other preferred embodiments, the parvovirus particlesof the present invention are administered to the lungs.

The parvovirus vectors disclosed herein may be administered to the lungsof a subject by any suitable means, but are preferably administered byadministering an aerosol suspension of respirable particles comprised ofthe inventive parvovirus vectors, which the subject inhales. Therespirable particles may be liquid or solid. Aerosols of liquidparticles comprising the inventive parvovirus vectors may be produced byany suitable means, such as with a pressure-driven aerosol nebulizer oran ultrasonic nebulizer, as is known to those of skill in the art. See,e.g., U.S. Pat. No. 4,501,729. Aerosols of solid particles comprisingthe inventive virus vectors may likewise be produced with any solidparticulate medicament aerosol generator, by techniques known in thepharmaceutical art.

Dosages of the inventive parvovirus particles will depend upon the modeof administration, the disease or condition to be treated, theindividual subject's condition, the particular virus vector, and thegene to be delivered, and can be determined in a routine manner.Exemplary doses for achieving therapeutic effects are virus titers of atleast about 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², 10³, 10¹⁴, 10¹⁵transducing units or more, preferably about 10⁸-10¹³ transducing units,yet more preferably 10¹² transducing units.

In particular embodiments, the inventive parvovirus particles areadministered as part of a method of treating cancer or tumors byadministering anti-cancer agents (e.g., cytokines) or a cancer or tumorantigen. The parvovirus particle may be administered to a cell in vitroor to a subject in vivo or by using ex vivo methods, as described hereinand known in the art.

The term “cancer” has its understood meaning in the art, for example, anuncontrolled growth of tissue that has the potential to spread todistant sites of the body (i.e., metastasize). Exemplary cancersinclude, but are not limited to, leukemias, lymphomas, colon cancer,renal cancer, liver cancer, breast cancer, lung cancer, prostate cancer,ovarian cancer, melanoma, and the like. Preferred are methods oftreating and preventing tumor-forming cancers. The term “tumor” is alsounderstood in the art, for example, as an abnormal mass ofundifferentiated cells within a multicellular organism. Tumors can bemalignant or benign. Preferably, the inventive methods disclosed hereinare used to prevent and treat malignant tumors.

Cancer and tumor antigens according to the present invention have beendescribed hereinabove. By the terms “treating cancer” or “treatment ofcancer”, it is intended that the severity of the cancer is reduced orthe cancer is at least partially eliminated. Preferably, these termsindicate that metastasis of the cancer is reduced or at least partiallyeliminated. It is further preferred that these terms indicate thatgrowth of metastatic nodules (e.g., after surgical removal of a primarytumor) is reduced or at least partially eliminated. By the terms“prevention of cancer” or “preventing cancer” it is intended that theinventive methods at least partially eliminate or reduce the incidenceor onset of cancer. Alternatively stated, the present methods slow,control, decrease the likelihood or probability, or delay the onset ofcancer in the subject.

Likewise, by the terms “treating tumors” or “treatment of tumors”, it isintended that the severity of the tumor is reduced or the tumor is atleast partially eliminated. Preferably, these terms are intended to meanthat metastasis of the tumor is reduced or at least partiallyeliminated. It is also preferred that these terms indicate that growthof metastatic nodules (e.g., after surgical removal of a primary tumor)is reduced or at least partially eliminated. By the terms “prevention oftumors” or “preventing tumors” it is intended that the inventive methodsat least partially eliminate or reduce the incidence or onset of tumors.Alternatively stated, the present methods slow, control, decrease thelikelihood or probability, or delay the onset of tumors in the subject.

In other embodiments, cells may be removed from a subject with cancer ora tumor and contacted with the parvovirus particles of the invention.The modified cell is then administered to the subject, whereby an immuneresponse against the cancer or tumor antigen is elicited. This method isparticularly advantageously employed with immunocompromised subjectsthat cannot mount a sufficient immune response in vivo (i.e., cannotproduce enhancing antibodies in sufficient quantities).

It is known in the art that immune responses may be enhanced byimmunomodulatory cytokines (e.g., α-interferon, β-interferon,γ-interferon, ω-interferon, τ-interferon, interleukin-1α,interleukin-1β, interleukin-2, interleukin-3, interleukin-4, interleukin5, interleukin-6, interleukin-7, interleukin-8, interleukin-9,interleukin-10, interleukin-11, interleukin 12, interleukin-13,interleukin-14, interleukin-18, B cell Growth factor, CD40 Ligand, tumornecrosis factor-α, tumor necrosis factor-β, monocyte chemoattractantprotein-1, granulocyte-macrophage colony stimulating factor, andlymphotoxin). Accordingly, in particular embodiments of the invention,immunomodulatory cytokines (preferably, CTL inductive cytokines) areadministered to a subject in conjunction with the methods describedherein for producing an immune response or providing immunotherapy.

Cytokines may be administered by any method known in the art. Exogenouscytokines may be administered to the subject, or alternatively, anucleotide sequence encoding a cytokine may be delivered to the subjectusing a suitable vector, and the cytokine produced in vivo.

Having now described the invention, the same will be illustrated withreference to certain examples, which are included herein forillustration purposes only, and which are not intended to be limiting ofthe invention.

EXAMPLE 1 Materials and Methods

Plasmids. The rAAV plasmids expressing green fluorescent protein (GFP)were constructed from the previously described pTR_(Bs)UF-2 (a gift fromNick Muzyczka). First, the humanized GFP coding sequence was replacedwith the enhanced GFP (eGFP) (Clonetech) to create the plasmid,pTR-CMV-GFPneo. This plasmid generated the rAAV-GFPneo vector. Second,the Sal I fragment containing the neo coding region and SV40 promoterwas deleted to create pTR-CMV-GFP. The vector from this plasmid wasreferred to as rAAV-GFP in this report.

The plasmid, p43mEpo, a gift from Barry Byrne, contained the mouseerythropoietin gene under the control of the CMV promoter and generateda rAAV replicon (rAAVmEpo) of less than half the wtAAV length. A longerversion of this construct (pmEpo-λ) was made by inserting the 2.3 kbHind III fragment from λ phage into a Cla I site between thepolyadenylation signal and the downstream AAV terminal repeat. TherAAV-LacZ vector was generated from pDX11-LacZ, which has been describedelsewhere (McCown et al., (1996) Brain Research 713:99).

Viral vectors. Viral Vectors were generated in 293 cells (10⁸-10⁹ cellsper prep) by co-transfecting 3 plasmids containing: 1) the specific rAAVconstruct, 2) the AAV rep and cap genes (pACG), or 3) the essentialadenovirus helper genes (pXX-6; Xiao et al., (1998) J. Virology72:2224). At 40 hr post-transfection, the cells were scraped into themedia and lysed by three freeze-thaw cycles. The lysates were incubatedat 37° C. with 2 μg/ml DNase I until flocculent debris was dispersed.The lysates were cleared by centrifugation and rAAV was precipitatedusing ammonium sulfate (Snyder et al., Production of recombinantadeno-associated virus vectors. In: Dracopoli et al., editors. CurrentProtocols in Human Genetics. New York: John Wiley & Sons Ltd.: 1996. p.12.1.1-12.2.23). The virus ppt. was resuspended with 8 ml 10 mM Tris pH8.0, 1 mM MgCl₂ and cesium chloride was added to reach a final densityof 1.4 g/cm³ and a final volume 12.5 ml. The solution was centrifugedfor 36 hrs at 38 krpm in an SW41 rotor. Fractions (0.75 ml) werecollected by puncturing with a hypodermic needle at the bottom of eachtube and pumping the liquid to a fraction collector. The vectors werestored at 4° C. in cesium chloride.

Virion DNA (vDNA) was extracted from 10 μl of each fraction by digestionin 50 μl reactions containing 0.4 mg/ml protease K, 1% sarkosyl, and 10mM EDTA at 50° C. for 1 hour, followed by phenol/chloroform extraction.The samples were diluted 3-fold with water and precipitated with ethanolfor analysis by alkaline agarose gel electrophoresis and Southern blothybridization.

Cells and infections. HeLa and HEK 293 cells were grown in DMEM mediacontaining 10% FBS and Pen/Strep. Viral vector stocks were diluted inmedia before adding to sub-confluent cultures and left on the cellsuntil GFP transduction was observed by fluorescence microscopy at 24hours post-infection.

For expression of erythropoietin in mouse livers, 200 μl normal saline,containing 2×10¹⁰ physical particles of either conventional rAAV orduplexed virus (scAAV), was injected directly into the portal veins of10 week old Balb-c ByJ mice (Jackson Laboratory). Blood samples werecollected by retro-orbital phlebotomy at the time of infection and at7-day intervals for determination of hematocrit.

EXAMPLE 2 Generation of Duplexed Vectors

A rAAV plasmid construct (pTR-CMV-GFP), with a replicon size of 2299nucleotides, was used to generate a viral vector stock (rAAV-GFP) byconventional methods. The predicted size of the dimeric replicative formof this vector was 4474 nucleotides (FIG. 1), which was 95.6% of the wtAAV genome length. The viral vectors were fractionated by isopycnicgradient centrifugation in CsCl and the vDNA content of each fractionwas analyzed on alkaline agarose gels (FIG. 2). Phospholmager scans wereused to quantify the vDNA specific bands from each fraction. Underdenaturing conditions, the self-complementary dimer DNA (FIG. 2, panela, fractions 10-13) ran at approximately twice the length of themonomeric genome. The hybridizing material in fractions 2-4 isunpackaged replicative form DNA that sediments at the bottom of thegradient. Although a DNase step was included in the vector purification(see methods), the treatment was not intended to be exhaustive and thismaterial proved to be DNase sensitive in subsequent experiments whilethe material in fractions 10-14 was DNase resistant (data not shown).Vectors containing mostly dimeric DNA genomes (fractions 10 and 11) weredesignated as duplexed or “self-complementary” virus (scAAV). Theinverted repeat structure of these molecules was confirmed byrestriction enzyme digestion (data not shown).

Two additional rAAV vectors (FIG. 1) were generated and purified inparallel, and analyzed in the same manner (FIG. 2, panels b and c). Thefirst, rAAV-GFPneo, contained a neo gene in addition to the GFP and hada replicating genome length of 3398 nucleotides. This was 72.6% of thewtAAV genome size, and was too large to be packaged as a dimer. Thesecond was a 4898 nucleotide rAAV-CMV-LacZ construct, which was slightlylarger (104.7%) than wtAAV genome size, but within the limit forefficient packaging (Dong et al., (1996) Human Gene Therapy 7:2101). Thelower density, higher mobility hybridizing material in fractions 14 and15 (FIG. 2, panel c) comprised genomes which had undergone deletions andthese fractions were not used in subsequent experiments.

EXAMPLE 3 Transduction with Duplexed Versus Monomeric Vectors andEffects of Ad Co-Infection

The transducing efficiency of the scAAV-GFP (FIG. 2, panel a, fraction11) was compared with the homologous monomer (fraction 13), as well asthe GFPneo and LacZ vectors (FIG. 2, panels b and c, fractions 13 and12, respectively) in HeLa cells infected at low multiplicity (FIG. 3).The particle numbers were calculated from the specific, full-length vDNAPhospholmager signals in each fraction on the Southern blot, aftercorrection for monomeric versus dimeric DNA copy number. Thus, eachduplexed virus contains two copies of the transgene as a singlemolecule, in the inverted repeat orientation, while each monomericparticle contains one single-stranded copy.

The scAAV-GFP vector (fraction 11), containing approximately 90% dimervirus, yielded a 5.9:1 ratio of physical particles to transducing units,thus bearing out the prediction of high transducing efficiency. Fraction13 from the same gradient, conversely containing approximately 80-90%monomer virus, had a 24.6:1 particle to transducing unit ratio. This4-fold difference in efficiency represented a minimum difference when itwas considered that the dimer contamination in the monomer fractionwould have a greater impact on its transducing potential than themonomer component would contribute to the dimer fraction. In contrast,the monomeric ssDNA GFPneo and LacZ vectors had particle to transducingunit ratios of 125:1 and 828:1, respectively, comparable to previouslyreported efficiencies for these vectors (Fisher et al., (1996) J.Virology 70:520; Zolotukhin et al., (1999) Gene Therapy 6:973).

The transducing efficiency of conventional rAAV vectors can be greatlyenhanced (up to 100-fold) by co-infection with Ad, or by treatment withDNA damaging agents or other types of cell stress. This enhancement hadbeen associated with the cell-mediated transformation of the ssDNAgenome into active ds-DNA transcription templates. Because the duplexedvector contains the two complementary strands packaged as a singlemolecule, it was predicted that transduction would be independent ofenhancement by adenovirus. This was largely the case when HeLa cellswere co-infected with the duplexed vectors and 5 infectious units percell of adenovirus (FIG. 3). The number of GFP positive cells in theduplexed virus infected cultures was increased by only 1.6-fold, aneffect which could be attributed to the transcriptional effects ofadenovirus infection on the activity of the CMV promoter as previouslyreported (Clesham et al., (1998) Gene Therapy 5:174; Loser et al.,(1998) J. Virology 72:180). The monomer vector transduction rate wasincreased 2.4-fold by Ad co-infection, while the GFPneo and LacZ vectorswere induced 6.0-fold and 12.8-fold, respectively.

In sum, in cultured HeLa cells, the duplexed vector was greater thanfour-fold more efficient than the homologous vector containing only amonomeric ss-DNA genome. This difference would likely be greater if notfor the approximately 10-20% contamination of monomer fractions withdimer vectors. Consistent with this interpretation, the duplexed vectorwas 20-fold more efficient than a conventional rAAV-GFPneo vector and140-fold more efficient than a rAAV-LacZ vector.

EXAMPLE 4 Transduction with Duplexed Vectors In the Absence of Host CellDNA Synthesis

Because the vDNA of the duplexed vectors contained both DNA strands on asingle molecule, allowing efficient reannealing upon uncoating, it waspredicted that these vectors would obviate the role of host-cell DNAsynthesis in transduction. The scAAV-GFP vector was compared with thehomologous monomer, and the GFPneo vector, in HeLa cells pretreated withhydroxyurea (HU) 24 hours before infection to inhibit host cell DNAsynthesis. Hydroxyurea treatment was continued, uninterrupted, at thesame concentrations following infection and maintained on the cells forthe following 24 hours, until GFP transduction was scored.

Transduction from the scAAV-GFP was stimulated by up to 1.9 fold inresponse to increasing concentrations of HU (FIG. 4). This stimulation,similar in magnitude to that observed with Ad co-infection, was probablyaffected through a combination of transcriptional transactivation of theCMV promoter brought about by cell stress, and the accumulation of GFPin the non-dividing cells. In contrast, transduction from the homologousmonomer vector fraction was stimulated at the lowest HU concentrationand inhibited at higher concentrations. The residual transducingactivity from the monomer vector at higher HU concentrations, at a levelapproximately 5-fold lower than that of the duplexed virus fraction, isconsistent with the 10-20% contamination of the monomer fractions withdimer containing particles (FIG. 2, panel a). The rAAV-GFPneo vectortransduction was inhibited greater than 10-fold under the sameconditions. Identical results were obtained by treatment withaphidicolin, a polymerase α/δ specific inhibitor (FIG. 4, panel b). Thisconfirmed the hypothesis that duplexed vector transduction wasindependent of host-cell DNA synthesis.

EXAMPLE 5 Transduction by Duplexed Vectors in vivo

A different reporter was used for the comparison of duplexed andconventional single-stranded rAAV efficiency in vivo. Thedimer-producing construct contained only the mouse erythropoietin gene(mEpo) transcribed from the CMV promoter. The size of the replicatingelement of this minimal vector was 2248 nucleotides. The dimeric form ofthis molecule, 4372 nucleotides in length (FIG. 1), was 93% of the wtAAVgenome size, and was readily packaged. A second construct contained theidentical transgene, with the addition of a downstream heterologoussequence (λ phage) to bring the size of the recombinant vector to 4570nucleotides, or 98% of the wtAAV genome size. Previous studies have usedlambda phage DNA as a stuffer without deleterious effects on the vector(Muzyczka et al., (1992) Curr. Top. Microbiol. Immunol. 158:97). Bothvectors were purified by heparin-agarose chromatography. The smallervector was additionally purified on a CsCl gradient to isolate dimericDNA-containing virions (not shown). The two vector stocks werequantified using Southern blots from alkaline agarose gels to determinethe number of DNA-containing particles. In this case, approximately 25%of the particles in the dimer fraction contained two separate monomergenomes. Because they could not be separated from true dimer by density,and because their behavior has not been characterized, these werecounted as dimer particles, for the purpose of comparison to thefull-length vector, such that the dimer effect might only beunderestimated rather than overestimated.

Equal numbers of physical rAAV particles (2×10¹⁰ per animal in 200 μlnormal saline) were administered to mice by portal vein injection. Theexpression of the mEpo gene was evaluated by observing changes inhematocrit at 7-day intervals. Control mice received either intraportalsaline injections or were not operated, but phlebotomized at 7-dayintervals. Mice receiving the duplexed vector responded with a rapidincrease in hematocrit (FIG. 5), and with continuing increases over thefollowing two weeks. Considering the lag time between expression oferythropoietin and the production of red blood cells, this suggestedthat the duplexed vector was expressed at high levels within the firstweek. Mice which received the full-length, ssDNA vector did not show asignificant increase in hematocrit until 21 days post-injection, and didnot reach levels comparable to the animals treated with duplexed vectorover the course of the experiment.

Infecting mice with scAAVmEpo leads to a faster response, and a greaterrise in hematocrit, than the full-length ssDNA vector carrying the samegene. These results support our observations in cultured cells and isconsistent with the view that the dimeric vectors are ready to expressthe transgene immediately upon uncoating and entry into the nucleus. Thehigher levels of expression ultimately achieved may reflect theinability of many infects cells to form dsDNA from conventional rAAVand/or the loss/degradation of ssvDNA prior to the formation of duplex(Miao et al., (1998) Nature Genetics 19:13).

As we have demonstrated by pre-treatment of cells with HU, transductionwith the scAAV vector is independent of host cell DNA synthesis. Theability to transduce cells in the absence of DNA synthesis represents afundamental departure in the biology of scAAV vectors from the parentvirus, allowing them to function under circumstances where conventionalrAAV vectors would fail. Certain cell types are extremely inefficientfor rAAV transduction ostensibly due to the inability to synthesize orrecruit a complementary strand (Fisher et al., (1996) J. Virology70:520; Alexander et al., (1996) Human Gene Therapy 7:841; Miao et al.,(1998) Nature Genetics 19:13). The scAAV suffers no such limitation andcan be used with marker genes to directly determine whether a cell ispermissive for rAAV transduction in all other steps irrespective of DNAsynthesis.

Regardless of the ability of the target cell to make the rAAVcomplementary strand, it is clear that these reagents provide analternative AAV delivery system for genes that may require rapid onset.More importantly, our data suggest that scAAV vectors achieve overallhigher levels of therapeutic product when an identical number ofparticles is administered. Thus, scAAV vectors will prove useful where amore timely, robust, or quantitative response to vector dose isrequired. The potential for attaining critical levels of transgeneexpression at minimal dose is also important with respect to vectorproduction requirements for clinical trials and for minimizing patientexposure to virus.

EXAMPLE 6 Improved Substrates for Producing Duplexed Parvovirus Vectors

To streamline the production of duplexed vector stocks, and to eliminatethe complications of mixed populations of duplex and monomer genomes, amutant vector was created which generates only the dimer genomes (FIG.6), This construct has a mutation in one TR, such that the Rep nickingsite (trs) is deleted, while the other TR is wild type. The effect isthat rolling hairpin replication initiates from the wt end of thegenome, proceeds through the mutant end without terminal resolution, andthen continues back across the genome again to create the dimer. The endproduct is a self-complementary genome with the mutant TR in the middleand wt TRs now at each end. Replication and packaging of this moleculethen proceeds as normal from the wt TRs, except that the dimericstructure is maintained in each round.

Vector stocks of both rAAV-CMV-GFP-Hpa-trs and rAAV-CMV-mEpo-Hpa-trshave been generated using this mutant background and analyzed theproducts on CsCl gradients as above (FIG. 7). These constructs produceapproximately 90% duplexed vectors. This will allow greater yields ofthe duplexed parvovirus vector and the use of iodixanol/heparinpurification for these vectors without the additional step of CsCldensity gradient purification.

The plasmid construct used to generate these vectors contained adeletion in the 5′ TR, relative to the coding strand of the expressedtransgene. This deletion includes all the D element and 3 by of the Aelement, thus spanning the nicking site (FIG. 6). All AAV sequencesbetween the remainder of the A element and the transgene are deleted.This precludes homologous recombination between sequences flanking themutated TR and the wt TR, thus reducing the possibility of geneconversion as described by Samulski et al., (1983) Cell 33:135. Thisdeletion was constructed by cutting at unique restriction sitesimmediately 5′ to the transgene (KpnI) and within the Amp gene of thebacterial plasmid sequences (XmnI). The fragment removed, containing oneTR, was replaced with a fragment from a second rAAV plasmid, which hadbeen cut at the same site within the Amp gene, and at a synthetic HpaIsite previously inserted into the BalI site to the left of the A/Djunction.

In an alternative embodiment, a template for preferentially producingduplexed vector is generated with a resolvable AAV TR at one end and amodified AAV TR is produced by inserting a sequence into the TR. In oneparticular embodiment, the wt AAV plasmid psub201 is used to producethis template (Samulski et al., (1987) J. Virology 61:3096). Thisconstruct contains a unique pair of Xba I sites as well as Pvul I sitesflanking the viral TRs. Two AAV plasmid intermediates derived frompsub201, Hpa7 and Hpa9, have a unique HpaI linker (CCAATTGG) inserted atthe Bal I site between nucleotide 121 and 122 (Hpa9) and between 4554and 4555 (Hpa7) in the TR sequence of the AAV genome, respectively(Xiao, X., (1996), “Characterization of Adeno-associated virus (AAV) DNAreplication and integration”, Ph.D. Dissertation, University ofPittsburgh, Pittsburgh, Pa.). Insertion of these linkers displaces thewt AAV nicking site inward away from the native position, resulting inan inability to be resolved by the AAV Rep protein after replication.

These substrates accumulate a dimeric intermediate until gene conversiontakes place. Digestion of Hpa7 or Hpa9 with HpaI restriction enzyme pluspartial digestion with Xba I, results in novel TRs lacking the wt AAVnicking site as well as the D element (from the left for Hpa9 and fromthe right for Hpa7). This substrate is not suitable for gene conversionas described by Samulski et al., (1983) Cell 33:135, due to the absenceof the D element, and continues to accumulate a dimeric replicationintermediate after viral infection. When starting with a molecule thatis half-size or less of the wtAAV genome, this intermediate ispreferentially packaged by AAV capsids. These molecules are dimeric inform (covalently linked through the modified TR), more specifically,because they are self-complementary they provide a unique source ofparvovirus vectors carrying double-stranded substrates. These vectorparticles bypass the rate-limiting step required for all currentlyutilized AAV vectors, namely, second-strand synthesis (see Ferrari etal., (1996) J. Virology 70:3227-34).

EXAMPLE 7 Transduction of Dendritic Cells

Dendritic cells (DC) are postulated to play important roles in antigenpresentation and initiation of several T cell dependent immuneresponses. DC have been demonstrated to be more potentantigen-presenting cells (APC) than are macrophages or monocytes.Moreover, it has been reported that DC stimulate T cell proliferation upto ten-fold more efficiently than do monocytes (Guyre et al., (1997)Cancer Immunol. Immunother. 45:146, 147 col. 2). Accordingly, there arenumerous efforts to target vectors to dendritic cells so as to produce amore effective immune response. It has previously been reported that DCare refractory to AAV vectors (Jooss et al., (1998) J. Virology72:4212).

DC from two human patients were obtained and cultured in vitro. Cellsfrom each patient were transduced with wtAAV-GFP vector or pHpa7GFP(duplexed vector, described in Example 1) at a MOI of 10. No GFPexpression was detected in cells transduced with wtAAV-GFP after 7 days.In contrast, GFP expression was observed in 5-15% DC transduced withdimeric pHpa7GFP vector.

These results suggest that the limiting step for wtAAV transduction ofDC is at level of host cell ability to mediate second-strand synthesis.The parvovirus vectors of the invention appear to obviate this step byproviding the cell with a double-stranded substrate. Accordingly, theinventive dimeric parvovirus vectors have a different (e.g., broader)tropism and target cell range than do wtAAV vectors.

EXAMPLE 8 In vivo Administration of pHpa7GFP

To evaluate the tropism of the duplexed vectors in vivo, mice areadministered intramuscularly (inn) with approximately 1.5×10¹¹ of thewtAAV-GFP or pHPA7GFP vectors described in Example 7. At various timespost-administration (e.g., 4, 8, 16, 32, 64 days, etc.), mice aresacrificed and autopsies performed to determine transgene expression invarious host cells and tissues. The onset, kinetics and persistence ofexpression are also evaluated and compared for the wtAAV anddouble-stranded vectors. Of particular interest are cells that aretypically refractory to wtAAV vectors such as bone marrow stem cells,astrocytes, and pulmonary epithelial cells. Also of interest arenon-replicating or slowly-replicating cells that inefficiently supportsecond-strand AAV synthesis such as muscle, liver and cells of thecentral nervous system.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity andunderstanding, it will be apparent that certain changes andmodifications may be practiced within the scope of the appended claimsand equivalents thereof.

1. A parvovirus particle comprising: a parvovirus capsid; and a vectorgenome comprising in the 5′ to 3′ direction: (i) a 5′ parvovirusterminal repeat; (ii) a first heterologous nucleotide sequence; (iii) aninverted terminal repeat that forms a hairpin structure, does notcomprise a functional parvovirus terminal resolution site (trs), and isresolved by Rep protein to a lesser extent as compared with the 5′parvovirus terminal repeat and a 3′ parvovirus terminal repeat; (iv) aseparate heterologous nucleotide sequence; and (v) the 3′ parvovirusterminal repeat; wherein the first and the separate heterologousnucleotide sequences are essentially self-complementary.
 2. Theparvovirus particle of claim 1, wherein the 5′ and the 3′ parvovirusterminal repeats are 5′ and 3′ AAV terminal repeats.
 3. The parvovirusparticle of claim 2, wherein the 5′ and the 3′ AAV terminal repeats areselected from the group consisting of 5′ and 3′ AAV1, AAV2, AAV3, AAV4,AAV5 and AAV6 terminal repeats.
 4. The parvovirus particle of claim 1,wherein the vector genome is approximately the size of a wild-type AAVgenome.
 5. The parvovirus particle of claim 1, wherein a polypeptide isencoded by the first and the separate heterologous nucleotide sequences.6. The parvovirus particle of claim 5, wherein the polypeptide is atherapeutic polypeptide.
 7. The parvovirus particle of claim 5, whereinthe polypeptide is an immunogenic polypeptide.
 8. The parvovirusparticle of claim 5, wherein the polypeptide is an endostatin, anangiostatin, a superoxide dismutase, an erythropoietin, a monoclonalantibody, a Factor IX, a Factor X, a lysosomal enzyme, a globin, aleptin, a catalase, a tyrosine hydroxylase, a cytokine, a peptide growthfactor, a hormone, a receptor, a suicide gene product, a tumorsuppressor gene product or an ornithine transcarbamylase.
 9. Theparvovirus particle of claim 5, wherein the polypeptide is a cancer or atumor antigen.
 10. The parvovirus particle of claim 5, wherein thepolypeptide is a bacterial antigen, a viral antigen, a protozoanantigen, or a parasite antigen.
 11. The parvovirus particle of claim 1,wherein the first and the separate heterologous nucleotide sequencesencode an antisense nucleic acid, a ribozyme, an RNA that effectsspliceosome-mediated trans-splicing, an interfering RNA (RNAi), or aguide RNA.
 12. The parvovirus particle of claim 1, wherein saidparvovirus capsid is an AAV capsid.
 13. The parvovirus particle of claim12, wherein said parvovirus capsid is selected from the group consistingof an AAV1, an AAV2, an AAV3, an AAV4, an AAV5 and an AAV6 capsid. 14.The parvovirus particle of claim 1, wherein the 5′ and the 3′ halves ofthe vector genome are essentially completely complementary to eachother.
 15. A pharmaceutical formulation comprising a plurality of theparvovirus particles of claim 1 in a pharmaceutically acceptablecarrier.
 16. A parvovirus particle comprising: an AAV capsid; and avector genome comprising in the 5′ to 3′ direction: (a) a 5′ AAVterminal repeat; (ii) a first heterologous nucleotide sequence; (iii) aninverted terminal repeat that forms a hairpin structure, does notcomprise a functional AAV terminal resolution site (trs), and isresolved by Rep protein to a lesser extent as compared to the 5′ AAVterminal repeat and a 3′ AAV terminal repeat; (iv) a separateheterologous nucleotide sequence; and (v) the 3′ AAV terminal repeat;wherein the first and the separate heterologous nucleotide sequences areessentially self-complementary.
 17. The parvovirus particle of claim 16,wherein the vector genome is approximately the size of a wild-type AAVgenome.
 18. The parvovirus particle of claim 16, wherein a polypeptideis encoded by the first and separate heterologous nucleotide sequences.19. The parvovirus particle of claim 18, wherein the polypeptide is atherapeutic polypeptide.
 20. The parvovirus particle of claim 18,wherein the polypeptide is an immunogenic polypeptide.
 21. Theparvovirus particle of claim 18, wherein the polypeptide is anendostatin, an angiostatin, a superoxide dismutase, an erythropoietin, amonoclonal antibody, a Factor IX, a Factor X, a lysosomal enzyme,globin, a leptin, a catalase, a tyrosine hydroxylase, a cytokine, apeptide growth factor, a hormone, a receptor, a suicide gene product, atumor suppressor gene product or an ornithine transcarbamylase.
 22. Theparvovirus particle of claim 18, wherein the polypeptide is a cancer ora tumor antigen.
 23. The parvovirus particle of claim 18, wherein thepolypeptide is a bacterial antigen, a viral antigen, a protozoanantigen, or a parasite antigen.
 24. The parvovirus particle of claim 16,wherein the first and separate heterologous nucleotide sequences encodean antisense nucleic acid, a ribozyme, an RNA that effectsspliceosome-mediated trans-splicing, an interfering RNA (RNAi), or aguide RNA.
 25. A pharmaceutical formulation comprising a plurality ofthe parvovirus particles of claim 16 in a pharmaceutically acceptablecarrier.
 26. A method of delivering the vector genome to a mammaliancell, comprising contacting the mammalian cell with the parvovirusparticle according to claim 1 under conditions sufficient for theparvovirus particle to enter the mammalian cell.
 27. The method of claim26, wherein the cell is selected from the group consisting of a cancercell, a tumor cell, a brain cell, a muscle cell, an airway epithelialcell, a liver cell, a dendritic cell, and an eye cell.
 28. The method ofclaim 26, wherein a polypeptide is encoded by the first and separateheterologous nucleotide sequences.
 29. The method of claim 28, whereinthe polypeptide is a therapeutic polypeptide.
 30. The method of claim28, wherein the polypeptide is an immunogenic polypeptide.
 31. Themethod of claim 28, wherein the polypeptide is an endostatin, anangiostatin, a superoxide dismutase, an erythropoietin, a monoclonalantibody, a Factor IX, a Factor X, a lysosomal enzyme, a globin, aleptin, a catalase, a tyrosine hydroxylase, a cytokine, a peptide growthfactor, a hormone, a receptor, a suicide gene product, a tumorsuppressor gene product or an ornithine transcarbamylase.
 32. The methodof claim 28, wherein the polypeptide is a cancer or a tumor antigen. 33.The method of claim 28, wherein the polypeptide is a bacterial antigen,a viral antigen, a protozoan antigen, or a parasite antigen.
 34. Themethod of claim 26, wherein the vector genome encodes an antisensenucleic acid, a ribozyme, an RNA that effects spliceosome-mediatedtrans-splicing, an interfering RNA (RNAi), or a guide RNA.
 35. Themethod of claim 26, wherein the parvovirus capsid is an AAV capsid. 36.The method of claim 26, wherein the 5′ and the 3′ parvovirus terminalrepeats are 5′ and 3′ AAV repeats.
 37. A method of delivering the vectorgenome to a mammalian cell, comprising contacting the mammalian cellwith the parvovirus particle according to claim 16 under conditionssufficient for the parvovirus particle to enter the mammalian cell.